From 0d11e67e60d308cfad2888b9bf8ea5c10ee0094f Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 3 Apr 2023 21:08:48 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.graphql | 906 +- biolink-model.owl.ttl | 1321 +- biolink-model.proto | 851 +- biolink-model.shacl.ttl | 25842 +++++++++------- biolink-model.shexj | 81 +- biolink-model.ttl | 1869 +- biolink-modeln.shex | 15 +- biolink-modeln.shexj | 81 +- biolink/model.py | 118 +- biolink/pydanticmodel.py | 906 +- context.jsonld | 21 +- contextn.jsonld | 21 +- ...l_entity_ontogenic_association_config.yaml | 57 + ...cal_entity_part_of_association_config.yaml | 57 + golr-views/association_config.yaml | 57 + ...behavioral_feature_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...a_model_of_disease_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...mical_affects_gene_association_config.yaml | 57 + ...sesses_named_thing_association_config.yaml | 57 + ...uct_regulates_gene_association_config.yaml | 57 + ...l_gene_interaction_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...emical_to_chemical_association_config.yaml | 57 + ...hemical_derivation_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...hemical_to_pathway_association_config.yaml | 57 + .../contributor_association_config.yaml | 57 + ...enetic_inheritance_association_config.yaml | 57 + ...eature_to_location_association_config.yaml | 57 + ..._to_exposure_event_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + .../drug_to_gene_association_config.yaml | 57 + ...le_gene_to_disease_association_config.yaml | 57 + .../entity_to_disease_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...xon_to_transcript_relationship_config.yaml | 57 + ...e_event_to_outcome_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + golr-views/functional_association_config.yaml | 57 + ...a_model_of_disease_association_config.yaml | 57 + ...ributes_to_disease_association_config.yaml | 57 + .../gene_to_disease_association_config.yaml | 57 + ...to_expression_site_association_config.yaml | 57 + ..._gene_coexpression_association_config.yaml | 57 + ...ene_to_gene_family_association_config.yaml | 57 + ...e_to_gene_homology_association_config.yaml | 57 + ...e_to_gene_product_relationship_config.yaml | 57 + .../gene_to_go_term_association_config.yaml | 57 + .../gene_to_pathway_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + .../genomic_sequence_localization_config.yaml | 57 + ...a_model_of_disease_association_config.yaml | 57 + ...enotype_to_disease_association_config.yaml | 57 + .../genotype_to_gene_association_config.yaml | 57 + ...e_to_genotype_part_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...enotype_to_variant_association_config.yaml | 57 + ...ity_to_named_thing_association_config.yaml | 57 + ...biological_process_association_config.yaml | 57 + ...cellular_component_association_config.yaml | 57 + ...molecular_activity_association_config.yaml | 57 + ..._sample_derivation_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...to_chemical_entity_association_config.yaml | 57 + ...molecular_activity_association_config.yaml | 57 + ...ctivity_to_pathway_association_config.yaml | 57 + ...ood_of_named_thing_association_config.yaml | 57 + ..._to_organism_taxon_interaction_config.yaml | 57 + ..._organism_taxon_specialization_config.yaml | 57 + ...ganism_to_organism_association_config.yaml | 57 + ...a_model_of_disease_association_config.yaml | 57 + ...rwise_gene_to_gene_interaction_config.yaml | 57 + ...pairwise_molecular_interaction_config.yaml | 57 + ...tion_to_population_association_config.yaml | 57 + ...action_to_catalyst_association_config.yaml | 57 + ...ion_to_participant_association_config.yaml | 57 + golr-views/retrieval_source_config.yaml | 8 +- golr-views/sequence_association_config.yaml | 57 + .../sequence_feature_relationship_config.yaml | 57 + .../taxon_to_taxon_association_config.yaml | 57 + ...ranscript_to_gene_relationship_config.yaml | 57 + ...a_model_of_disease_association_config.yaml | 57 + ...variant_to_disease_association_config.yaml | 57 + .../variant_to_gene_association_config.yaml | 57 + ...to_gene_expression_association_config.yaml | 57 + ...phenotypic_feature_association_config.yaml | 57 + ...iant_to_population_association_config.yaml | 57 + ...entity_to_anatomical_entity_association.gv | 255 +- ...ntity_to_anatomical_entity_association.svg | 371 +- ...anatomical_entity_ontogenic_association.gv | 259 +- ...natomical_entity_ontogenic_association.svg | 381 +- ...o_anatomical_entity_part_of_association.gv | 258 +- ..._anatomical_entity_part_of_association.svg | 381 +- graphviz/association.gv | 239 +- graphviz/association.svg | 321 +- ...avior_to_behavioral_feature_association.gv | 306 +- ...vior_to_behavioral_feature_association.svg | 475 +- .../case_to_phenotypic_feature_association.gv | 286 +- ...case_to_phenotypic_feature_association.svg | 419 +- ..._line_as_a_model_of_disease_association.gv | 275 +- ...line_as_a_model_of_disease_association.svg | 401 +- ...sease_or_phenotypic_feature_association.gv | 248 +- ...ease_or_phenotypic_feature_association.svg | 353 +- graphviz/chemical_affects_gene_association.gv | 380 +- .../chemical_affects_gene_association.svg | 665 +- ...entity_assesses_named_thing_association.gv | 258 +- ...ntity_assesses_named_thing_association.svg | 381 +- ...gene_product_regulates_gene_association.gv | 264 +- ...ene_product_regulates_gene_association.svg | 401 +- .../chemical_gene_interaction_association.gv | 326 +- .../chemical_gene_interaction_association.svg | 537 +- ...sease_or_phenotypic_feature_association.gv | 242 +- ...ease_or_phenotypic_feature_association.svg | 351 +- ...sease_or_phenotypic_feature_association.gv | 240 +- ...ease_or_phenotypic_feature_association.svg | 349 +- graphviz/chemical_to_chemical_association.gv | 247 +- graphviz/chemical_to_chemical_association.svg | 341 +- ...ical_to_chemical_derivation_association.gv | 267 +- ...cal_to_chemical_derivation_association.svg | 401 +- ...sease_or_phenotypic_feature_association.gv | 246 +- ...ease_or_phenotypic_feature_association.svg | 343 +- graphviz/chemical_to_pathway_association.gv | 264 +- graphviz/chemical_to_pathway_association.svg | 377 +- graphviz/contributor_association.gv | 261 +- graphviz/contributor_association.svg | 393 +- ...ture_to_genetic_inheritance_association.gv | 247 +- ...ure_to_genetic_inheritance_association.svg | 349 +- ...notypic_feature_to_location_association.gv | 245 +- ...otypic_feature_to_location_association.svg | 339 +- .../disease_to_exposure_event_association.gv | 246 +- .../disease_to_exposure_event_association.svg | 331 +- ...sease_to_phenotypic_feature_association.gv | 311 +- ...ease_to_phenotypic_feature_association.svg | 483 +- graphviz/drug_to_gene_association.gv | 248 +- graphviz/drug_to_gene_association.svg | 341 +- .../druggable_gene_to_disease_association.gv | 295 +- .../druggable_gene_to_disease_association.svg | 449 +- graphviz/entity_to_disease_association.gv | 239 +- graphviz/entity_to_disease_association.svg | 329 +- ...ntity_to_phenotypic_feature_association.gv | 236 +- ...tity_to_phenotypic_feature_association.svg | 329 +- graphviz/exon_to_transcript_relationship.gv | 257 +- graphviz/exon_to_transcript_relationship.svg | 371 +- .../exposure_event_to_outcome_association.gv | 248 +- .../exposure_event_to_outcome_association.svg | 349 +- ...event_to_phenotypic_feature_association.gv | 297 +- ...vent_to_phenotypic_feature_association.svg | 457 +- graphviz/functional_association.gv | 257 +- graphviz/functional_association.svg | 371 +- .../gene_as_a_model_of_disease_association.gv | 288 +- ...gene_as_a_model_of_disease_association.svg | 421 +- ...that_contributes_to_disease_association.gv | 273 +- ...hat_contributes_to_disease_association.svg | 425 +- graphviz/gene_to_disease_association.gv | 289 +- graphviz/gene_to_disease_association.svg | 421 +- .../gene_to_expression_site_association.gv | 274 +- .../gene_to_expression_site_association.svg | 417 +- graphviz/gene_to_gene_association.gv | 257 +- graphviz/gene_to_gene_association.svg | 371 +- .../gene_to_gene_coexpression_association.gv | 289 +- .../gene_to_gene_coexpression_association.svg | 443 +- graphviz/gene_to_gene_family_association.gv | 262 +- graphviz/gene_to_gene_family_association.svg | 381 +- graphviz/gene_to_gene_homology_association.gv | 261 +- .../gene_to_gene_homology_association.svg | 381 +- graphviz/gene_to_gene_product_relationship.gv | 261 +- .../gene_to_gene_product_relationship.svg | 381 +- graphviz/gene_to_go_term_association.gv | 258 +- graphviz/gene_to_go_term_association.svg | 371 +- graphviz/gene_to_pathway_association.gv | 264 +- graphviz/gene_to_pathway_association.svg | 377 +- .../gene_to_phenotypic_feature_association.gv | 311 +- ...gene_to_phenotypic_feature_association.svg | 483 +- graphviz/genomic_sequence_localization.gv | 282 +- graphviz/genomic_sequence_localization.svg | 437 +- ...otype_as_a_model_of_disease_association.gv | 291 +- ...type_as_a_model_of_disease_association.svg | 435 +- graphviz/genotype_to_disease_association.gv | 293 +- graphviz/genotype_to_disease_association.svg | 435 +- graphviz/genotype_to_gene_association.gv | 261 +- graphviz/genotype_to_gene_association.svg | 381 +- .../genotype_to_genotype_part_association.gv | 260 +- .../genotype_to_genotype_part_association.svg | 381 +- ...otype_to_phenotypic_feature_association.gv | 307 +- ...type_to_phenotypic_feature_association.svg | 479 +- graphviz/genotype_to_variant_association.gv | 261 +- graphviz/genotype_to_variant_association.svg | 381 +- ...ntent_entity_to_named_thing_association.gv | 258 +- ...tent_entity_to_named_thing_association.svg | 381 +- ...chine_to_biological_process_association.gv | 259 +- ...hine_to_biological_process_association.svg | 375 +- ...chine_to_cellular_component_association.gv | 260 +- ...hine_to_cellular_component_association.svg | 375 +- ...chine_to_molecular_activity_association.gv | 259 +- ...hine_to_molecular_activity_association.svg | 375 +- .../material_sample_derivation_association.gv | 261 +- ...material_sample_derivation_association.svg | 381 +- ...sease_or_phenotypic_feature_association.gv | 244 +- ...ease_or_phenotypic_feature_association.svg | 335 +- ...activity_to_chemical_entity_association.gv | 255 +- ...ctivity_to_chemical_entity_association.svg | 371 +- ...ivity_to_molecular_activity_association.gv | 254 +- ...vity_to_molecular_activity_association.svg | 371 +- ...lecular_activity_to_pathway_association.gv | 260 +- ...ecular_activity_to_pathway_association.svg | 381 +- ...h_likelihood_of_named_thing_association.gv | 263 +- ..._likelihood_of_named_thing_association.svg | 403 +- ...ganism_taxon_to_environment_association.gv | 265 +- ...anism_taxon_to_environment_association.svg | 387 +- ...ism_taxon_to_organism_taxon_association.gv | 263 +- ...sm_taxon_to_organism_taxon_association.svg | 377 +- ...ism_taxon_to_organism_taxon_interaction.gv | 267 +- ...sm_taxon_to_organism_taxon_interaction.svg | 401 +- ..._taxon_to_organism_taxon_specialization.gv | 261 +- ...taxon_to_organism_taxon_specialization.svg | 381 +- graphviz/organism_to_organism_association.gv | 257 +- graphviz/organism_to_organism_association.svg | 371 +- ...ntity_as_a_model_of_disease_association.gv | 275 +- ...tity_as_a_model_of_disease_association.svg | 401 +- graphviz/pairwise_gene_to_gene_interaction.gv | 261 +- .../pairwise_gene_to_gene_interaction.svg | 381 +- graphviz/pairwise_molecular_interaction.gv | 261 +- graphviz/pairwise_molecular_interaction.svg | 403 +- .../population_to_population_association.gv | 261 +- .../population_to_population_association.svg | 381 +- graphviz/reaction_to_catalyst_association.gv | 277 +- graphviz/reaction_to_catalyst_association.svg | 409 +- .../reaction_to_participant_association.gv | 277 +- .../reaction_to_participant_association.svg | 409 +- graphviz/retrieval_source.gv | 56 +- graphviz/retrieval_source.svg | 70 +- graphviz/sequence_association.gv | 237 +- graphviz/sequence_association.svg | 321 +- graphviz/sequence_feature_relationship.gv | 257 +- graphviz/sequence_feature_relationship.svg | 371 +- ...variant_modulates_treatment_association.gv | 254 +- ...ariant_modulates_treatment_association.svg | 371 +- graphviz/taxon_to_taxon_association.gv | 257 +- graphviz/taxon_to_taxon_association.svg | 371 +- graphviz/transcript_to_gene_relationship.gv | 258 +- graphviz/transcript_to_gene_relationship.svg | 371 +- ...riant_as_a_model_of_disease_association.gv | 292 +- ...iant_as_a_model_of_disease_association.svg | 435 +- graphviz/variant_to_disease_association.gv | 291 +- graphviz/variant_to_disease_association.svg | 435 +- graphviz/variant_to_gene_association.gv | 251 +- graphviz/variant_to_gene_association.svg | 351 +- .../variant_to_gene_expression_association.gv | 277 +- ...variant_to_gene_expression_association.svg | 411 +- ...riant_to_phenotypic_feature_association.gv | 307 +- ...iant_to_phenotypic_feature_association.svg | 467 +- graphviz/variant_to_population_association.gv | 315 +- .../variant_to_population_association.svg | 473 +- json-schema/biolink-model.json | 2 +- 257 files changed, 62176 insertions(+), 28730 deletions(-) diff --git a/biolink-model.graphql b/biolink-model.graphql index 44157d6dc3..0e4412eab7 100644 --- a/biolink-model.graphql +++ b/biolink-model.graphql @@ -93,6 +93,17 @@ interface AnatomicalEntityToAnatomicalEntityAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: AnatomicalEntity! @@ -117,6 +128,17 @@ type AnatomicalEntityToAnatomicalEntityOntogenicAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: AnatomicalEntity! @@ -142,6 +164,17 @@ type AnatomicalEntityToAnatomicalEntityPartOfAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: AnatomicalEntity! @@ -201,6 +234,17 @@ type Association originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] } @@ -257,6 +301,17 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: Behavior! @@ -476,6 +531,17 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] frequencyQualifier: FrequencyValue @@ -536,6 +602,17 @@ type CellLineAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: CellLine! @@ -564,6 +641,17 @@ type CellLineToDiseaseOrPhenotypicFeatureAssociation implements CellLineToEntity originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: DiseaseOrPhenotypicFeature! @@ -620,6 +708,17 @@ type ChemicalAffectsGeneAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum @@ -678,6 +777,17 @@ type ChemicalEntityAssessesNamedThingAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: ChemicalEntity! @@ -707,6 +817,17 @@ type ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] objectDirectionQualifier: DirectionQualifierEnum @@ -759,6 +880,17 @@ type ChemicalGeneInteractionAssociation implements ChemicalToEntityAssociationMi originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum @@ -820,6 +952,17 @@ type ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation im originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] fDAAdverseEventLevel: FDAIDAAdverseEventEnum @@ -846,6 +989,17 @@ type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] fDAAdverseEventLevel: FDAIDAAdverseEventEnum @@ -888,6 +1042,17 @@ type ChemicalToChemicalAssociation implements ChemicalToEntityAssociationMixin originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: ChemicalEntity! @@ -911,6 +1076,17 @@ type ChemicalToChemicalDerivationAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] catalystQualifier: [MacromolecularMachineMixin] @@ -939,6 +1115,17 @@ type ChemicalToDiseaseOrPhenotypicFeatureAssociation implements ChemicalToEntity originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: DiseaseOrPhenotypicFeature! @@ -968,6 +1155,17 @@ type ChemicalToPathwayAssociation implements ChemicalToEntityAssociationMixin originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: ChemicalEntity! @@ -1249,6 +1447,17 @@ type ContributorAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: InformationContentEntity! @@ -1417,6 +1626,17 @@ type DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation implements Diseas originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -1443,6 +1663,17 @@ type DiseaseOrPhenotypicFeatureToLocationAssociation implements DiseaseOrPhenoty originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: AnatomicalEntity! @@ -1474,6 +1705,17 @@ type DiseaseToExposureEventAssociation implements DiseaseToEntityAssociationMixi originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] } @@ -1497,6 +1739,17 @@ type DiseaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureA originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: Disease! @@ -1575,6 +1828,17 @@ type DrugToGeneAssociation implements DrugToEntityAssociationMixin originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: GeneOrGeneProduct! @@ -1615,6 +1879,17 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: Disease! @@ -1658,6 +1933,17 @@ type EntityToDiseaseAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] fDAApprovalStatus: FDAApprovalStatusEnum @@ -1714,6 +2000,17 @@ type EntityToPhenotypicFeatureAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] fDAApprovalStatus: FDAApprovalStatusEnum @@ -1872,6 +2169,17 @@ type ExonToTranscriptRelationship originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: Exon! @@ -1905,6 +2213,17 @@ type ExposureEventToOutcomeAssociation implements EntityToOutcomeAssociationMixi originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] populationContextQualifier: PopulationOfIndividualOrganisms @@ -1931,6 +2250,17 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: ExposureEvent! @@ -2016,6 +2346,17 @@ type FunctionalAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MacromolecularMachineMixin! @@ -2058,6 +2399,17 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin, originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: Disease! @@ -2113,6 +2465,17 @@ type GeneHasVariantThatContributesToDiseaseAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] frequencyQualifier: FrequencyValue @@ -2162,6 +2525,17 @@ type GeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneTo originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: GeneOrGeneProduct! @@ -2194,6 +2568,17 @@ type GeneToExpressionSiteAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] stageQualifier: LifeStage @@ -2222,6 +2607,17 @@ interface GeneToGeneAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: GeneOrGeneProduct! @@ -2246,6 +2642,17 @@ type GeneToGeneCoexpressionAssociation implements GeneExpressionMixin originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: GeneOrGeneProduct! @@ -2275,6 +2682,17 @@ type GeneToGeneFamilyAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: Gene! @@ -2300,6 +2718,17 @@ type GeneToGeneHomologyAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: GeneOrGeneProduct! @@ -2325,6 +2754,17 @@ type GeneToGeneProductRelationship originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: Gene! @@ -2351,6 +2791,17 @@ type GeneToGoTermAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: Gene! @@ -2376,6 +2827,17 @@ type GeneToPathwayAssociation implements GeneToEntityAssociationMixin originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: GeneOrGeneProduct! @@ -2401,6 +2863,17 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: GeneOrGeneProduct! @@ -2487,6 +2960,17 @@ type GenomicSequenceLocalization originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] startInterbaseCoordinate: Integer @@ -2533,6 +3017,17 @@ type GenotypeAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -2561,6 +3056,17 @@ type GenotypeToDiseaseAssociation implements GenotypeToEntityAssociationMixin, E originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: NamedThing! @@ -2594,6 +3100,17 @@ type GenotypeToGeneAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -2619,6 +3136,17 @@ type GenotypeToGenotypePartAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -2645,6 +3173,17 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -2677,6 +3216,17 @@ type GenotypeToVariantAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -2843,6 +3393,17 @@ type InformationContentEntityToNamedThingAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: NamedThing! @@ -2919,6 +3480,17 @@ type MacromolecularMachineToBiologicalProcessAssociation implements Macromolecul originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MacromolecularMachineMixin! @@ -2944,6 +3516,17 @@ type MacromolecularMachineToCellularComponentAssociation implements Macromolecul originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MacromolecularMachineMixin! @@ -2974,6 +3557,17 @@ type MacromolecularMachineToMolecularActivityAssociation implements Macromolecul originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MacromolecularMachineMixin! @@ -3016,6 +3610,17 @@ type MaterialSampleDerivationAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MaterialSample! @@ -3044,6 +3649,17 @@ type MaterialSampleToDiseaseOrPhenotypicFeatureAssociation implements MaterialSa originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] } @@ -3117,6 +3733,17 @@ type MolecularActivityToChemicalEntityAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MolecularActivity! @@ -3142,6 +3769,17 @@ type MolecularActivityToMolecularActivityAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MolecularActivity! @@ -3166,6 +3804,17 @@ type MolecularActivityToPathwayAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: MolecularActivity! @@ -3251,6 +3900,17 @@ type NamedThingAssociatedWithLikelihoodOfNamedThingAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -3428,6 +4088,17 @@ type OrganismTaxonToEnvironmentAssociation implements OrganismTaxonToEntityAssoc originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: OrganismTaxon! @@ -3454,6 +4125,17 @@ type OrganismTaxonToOrganismTaxonAssociation implements OrganismTaxonToEntityAss originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: OrganismTaxon! @@ -3478,6 +4160,17 @@ type OrganismTaxonToOrganismTaxonInteraction originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] associatedEnvironmentalContext: String @@ -3504,6 +4197,17 @@ type OrganismTaxonToOrganismTaxonSpecialization originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: OrganismTaxon! @@ -3530,6 +4234,17 @@ type OrganismToOrganismAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: IndividualOrganism! @@ -3570,6 +4285,17 @@ type OrganismalEntityAsAModelOfDiseaseAssociation implements ModelToDiseaseAssoc originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: OrganismalEntity! @@ -3600,6 +4326,17 @@ type PairwiseGeneToGeneInteraction originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: GeneOrGeneProduct! @@ -3624,6 +4361,17 @@ type PairwiseMolecularInteraction originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] interactingMoleculesCategory: OntologyClass @@ -3887,6 +4635,17 @@ type PopulationToPopulationAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: PopulationOfIndividualOrganisms! @@ -4077,6 +4836,17 @@ type ReactionToCatalystAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] stoichiometry: Integer @@ -4105,6 +4875,17 @@ type ReactionToParticipantAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: ChemicalEntity! @@ -4184,9 +4965,9 @@ type RetrievalSource rights: String format: String creationDate: Date - resource: Uriorcurie! + resourceId: Uriorcurie! resourceRole: ResourceRoleEnum! - upstreamResources: Uriorcurie + upstreamResourceIds: Uriorcurie xref: [Uriorcurie] } @@ -4259,6 +5040,17 @@ type SequenceAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] } @@ -4282,6 +5074,17 @@ type SequenceFeatureRelationship originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: NucleicAcidEntity! @@ -4323,6 +5126,17 @@ interface SequenceVariantModulatesTreatmentAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: SequenceVariant! @@ -4553,6 +5367,17 @@ type TaxonToTaxonAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: OrganismTaxon! @@ -4626,6 +5451,17 @@ type TranscriptToGeneRelationship originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: Transcript! @@ -4682,6 +5518,17 @@ type VariantAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMix originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] predicate: PredicateType! @@ -4710,6 +5557,17 @@ type VariantToDiseaseAssociation implements VariantToEntityAssociationMixin, Ent originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: NamedThing! @@ -4744,6 +5602,17 @@ type VariantToGeneAssociation implements VariantToEntityAssociationMixin originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: Gene! @@ -4769,6 +5638,17 @@ type VariantToGeneExpressionAssociation implements GeneExpressionMixin originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] object: Gene! @@ -4799,6 +5679,17 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: SequenceVariant! @@ -4831,6 +5722,17 @@ type VariantToPopulationAssociation implements VariantToEntityAssociationMixin, originalSubject: String originalPredicate: Uriorcurie originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] subject: SequenceVariant! diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index 9296bf0668..fd208a9e87 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -108,11 +108,11 @@ biolink:VariantToEntityAssociationMixin ; dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ; pav:version "3.2.5" ; - linkml:generation_date "2023-03-30T15:48:59" ; + linkml:generation_date "2023-04-03T20:56:19" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2023-03-30T15:47:28" ; - linkml:source_file_size 341681 . + linkml:source_file_date "2023-04-03T20:54:34" ; + linkml:source_file_size 348255 . biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; @@ -146,6 +146,10 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -153,75 +157,71 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" . biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], biolink:Publication . biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:Behavior ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:BehavioralFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:BehavioralFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Behavior ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." . @@ -256,12 +256,12 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], - [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . @@ -273,32 +273,32 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -317,21 +317,21 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:CellLine ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:CellLine ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -347,52 +347,60 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; @@ -400,23 +408,15 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:CausalMechanismQualifierEnum ; owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" . @@ -439,6 +439,10 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -446,10 +450,6 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; owl:onClass biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -461,48 +461,48 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onClass biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:ChemicalToEntityAssociationMixin ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; @@ -522,8 +522,9 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; @@ -533,9 +534,8 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], biolink:ChemicalToChemicalAssociation ; skos:definition """A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF @@ -637,10 +637,6 @@ biolink:ContributorAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Agent ; owl:onProperty rdf:object ; @@ -649,6 +645,10 @@ biolink:ContributorAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:InformationContentEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" . @@ -671,13 +671,13 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneticInheritance ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." . @@ -702,10 +702,6 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Disease ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], @@ -713,26 +709,22 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:Disease ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; @@ -741,6 +733,14 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -770,16 +770,16 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; - owl:onProperty biolink:has_evidence ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:onProperty biolink:has_evidence ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseAssociation, biolink:GeneToEntityAssociationMixin . @@ -845,13 +845,13 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:temporal_context_qualifier ], biolink:Association, biolink:EntityToOutcomeAssociationMixin ; skos:definition "An association between an exposure event and an outcome." . @@ -860,40 +860,40 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ExposureEvent ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . @@ -925,10 +925,6 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -937,6 +933,10 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:onClass biolink:Disease ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], biolink:GeneToDiseaseAssociation . biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ; @@ -995,17 +995,13 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; @@ -1014,6 +1010,10 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" . @@ -1022,20 +1022,20 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -1047,6 +1047,10 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Gene ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -1054,10 +1058,6 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; owl:onClass biolink:GeneFamily ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Gene ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." . @@ -1065,7 +1065,7 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -1073,7 +1073,7 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" . @@ -1081,6 +1081,10 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Gene ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -1088,23 +1092,19 @@ biolink:GeneToGeneProductRelationship a owl:Class ; owl:onClass biolink:GeneProductMixin ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Gene ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" . biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OntologyClass ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OntologyClass ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; skos:exactMatch WBVocab:Gene-GO-Association . @@ -1112,13 +1112,13 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Pathway ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Pathway ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:GeneToEntityAssociationMixin ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." . @@ -1127,44 +1127,44 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -1189,19 +1189,19 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], biolink:Attribute, biolink:ExposureEvent, biolink:GeneGroupingMixin, @@ -1246,11 +1246,11 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" . @@ -1258,45 +1258,45 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -1395,10 +1395,6 @@ biolink:HospitalizationOutcome a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1406,6 +1402,10 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." . @@ -1450,16 +1450,16 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:MaterialSample ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:MaterialSample ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." . @@ -1481,13 +1481,13 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" . @@ -1495,11 +1495,11 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" . @@ -1507,10 +1507,6 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1518,6 +1514,10 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; owl:onClass biolink:Pathway ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." . @@ -1538,16 +1538,16 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:object_aspect_qualifier ], biolink:Association ; skos:definition "" . @@ -1580,16 +1580,16 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation . @@ -1597,14 +1597,6 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:associated_environmental_context ], @@ -1612,16 +1604,20 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" . biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1629,6 +1625,10 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" . @@ -1636,32 +1636,32 @@ biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:IndividualOrganism ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:IndividualOrganism ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:OrganismalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -1669,25 +1669,25 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" . @@ -1793,16 +1793,16 @@ biolink:PhysiologicalProcess a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a two populations" . @@ -1926,12 +1926,12 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -1943,7 +1943,7 @@ biolink:Serial a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . @@ -1993,16 +1993,16 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Class ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], + [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ] [ a owl:Restriction ; owl:onProperty biolink:has_attribute ; owl:someValuesFrom biolink:SocioeconomicAttribute ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." . @@ -2033,11 +2033,11 @@ biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -2087,22 +2087,22 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], biolink:GeneExpressionMixin, biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" . @@ -2113,26 +2113,10 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; @@ -2141,10 +2125,26 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:VariantToEntityAssociationMixin . @@ -2153,8 +2153,8 @@ biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -2170,11 +2170,11 @@ biolink:VariantToPopulationAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; @@ -2962,6 +2962,10 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:chapter ], @@ -2969,10 +2973,6 @@ biolink:BookChapter a owl:Class ; owl:onClass linkml:Uriorcurie ; owl:onProperty biolink:published_in ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:volume ], biolink:Publication . biolink:Case a owl:Class ; @@ -3132,9 +3132,9 @@ biolink:GeneFamily a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; @@ -3147,14 +3147,14 @@ biolink:GenotypeToDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -3225,20 +3225,20 @@ biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ReactionSideEnum ; - owl:onProperty biolink:reaction_side ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:stoichiometry ], + owl:onClass biolink:ReactionDirectionEnum ; + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ReactionDirectionEnum ; - owl:onProperty biolink:reaction_direction ], + owl:onClass biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:stoichiometry ], biolink:ChemicalToChemicalAssociation . biolink:SequenceAssociation a owl:Class ; @@ -3264,18 +3264,18 @@ biolink:SymbolType a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -3292,18 +3292,10 @@ biolink:VariantToDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -3312,6 +3304,14 @@ biolink:VariantToDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:VariantToEntityAssociationMixin ; @@ -3320,13 +3320,13 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:VariantToEntityAssociationMixin ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" . @@ -4805,12 +4805,53 @@ biolink:nutrient_of a owl:ObjectProperty ; owl:inverseOf biolink:has_nutrient ; skos:definition "holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)" . +biolink:object_category a owl:ObjectProperty ; + rdfs:label "object category" ; + rdfs:domain biolink:Association ; + rdfs:range biolink:OntologyClass ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value='biolink:Disease', description=\"The object category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Disease'.\")" . + +biolink:object_category_closure a owl:ObjectProperty ; + rdfs:label "object category closure" ; + rdfs:domain biolink:Association ; + rdfs:range biolink:OntologyClass ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value=\"['biolink:Disease', 'biolink:NamedThing']\", description='The object category closure of the association between the gene \\'BRCA1\\' and the disease \\'breast cancer\\' is the set of all biolink classes that are ancestors of \\'biolink:Disease\\' in the biolink model. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well.')" . + +biolink:object_closure a owl:ObjectProperty ; + rdfs:label "object closure" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:String ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value=\"['MONDO:0000167', 'MONDO:0005395']\", description='The object closure of the association between the gene \\'BRCA1\\' and the disease \\'breast cancer\\' is the set of all diseases that are ancestors of \\'breast cancer\\' in the MONDO ontology. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well.')" . + biolink:object_derivative_qualifier a owl:ObjectProperty ; rdfs:label "object derivative qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:derivative_qualifier . +biolink:object_label_closure a owl:ObjectProperty ; + rdfs:label "object label closure" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:String ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value=\"['breast cancer', 'cancer']\", description=\"The object label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'breast cancer' in the biolink model.\")" . + +biolink:object_namespace a owl:ObjectProperty ; + rdfs:label "object namespace" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:String ; + rdfs:subPropertyOf biolink:association_slot ; + skos:altLabel "object prefix" ; + skos:definition "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value='MONDO', description=\"The object namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'MONDO'.\")" . + biolink:occurs_in a owl:ObjectProperty ; rdfs:label "occurs in" ; rdfs:domain biolink:NamedThing ; @@ -5101,8 +5142,8 @@ biolink:resistance_associated_with a owl:ObjectProperty ; rdfs:subPropertyOf biolink:associated_with ; owl:inverseOf biolink:associated_with_resistance_to . -biolink:resource a owl:ObjectProperty ; - rdfs:label "resource" ; +biolink:resource_id a owl:ObjectProperty ; + rdfs:label "resource id" ; rdfs:domain biolink:RetrievalSource ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:node_property ; @@ -5129,6 +5170,11 @@ biolink:response_increased_by a owl:ObjectProperty ; rdfs:subPropertyOf biolink:response_affected_by ; owl:inverseOf biolink:increases_response_to . +biolink:retrieval_source_ids a owl:ObjectProperty ; + rdfs:label "retrieval source ids" ; + rdfs:range biolink:RetrievalSource ; + skos:definition "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." . + biolink:rights a owl:ObjectProperty ; rdfs:label "rights" ; rdfs:domain biolink:InformationContentEntity ; @@ -5186,6 +5232,46 @@ biolink:strand a owl:ObjectProperty ; skos:definition "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; skos:exactMatch gff3:strand . +biolink:subject_category a owl:ObjectProperty ; + rdfs:label "subject category" ; + rdfs:domain biolink:Association ; + rdfs:range biolink:OntologyClass ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value='biolink:Gene', description=\"The subject category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Gene'.\")" . + +biolink:subject_category_closure a owl:ObjectProperty ; + rdfs:label "subject category closure" ; + rdfs:domain biolink:Association ; + rdfs:range biolink:OntologyClass ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value=\"['biolink:Gene', 'biolink:NamedThing']\", description='The subject category closure of the association between the gene \\'BRCA1\\' and the disease \\'breast cancer\\' is the set of all biolink classes that are ancestors of \\'biolink:Gene\\' in the biolink model. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well.')" . + +biolink:subject_closure a owl:ObjectProperty ; + rdfs:label "subject closure" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:String ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." . + +biolink:subject_label_closure a owl:ObjectProperty ; + rdfs:label "subject label closure" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:String ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value=\"['BRACA1']\", description=\"The subject label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'BRCA1' in the biolink model. \")" . + +biolink:subject_namespace a owl:ObjectProperty ; + rdfs:label "subject namespace" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:String ; + rdfs:subPropertyOf biolink:association_slot ; + skos:altLabel "subject prefix" ; + skos:definition "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + linkml:examples "Example(value='NCBIGene', description=\"The subject namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'NCBIGene'.\")" . + biolink:summary a owl:ObjectProperty ; rdfs:label "summary" ; rdfs:domain biolink:Publication ; @@ -5327,8 +5413,8 @@ biolink:treats a owl:ObjectProperty ; biolink:canonical_predicate "True" ; biolink:opposite_of "contraindicated for" . -biolink:upstream_resources a owl:ObjectProperty ; - rdfs:label "upstream resources" ; +biolink:upstream_resource_ids a owl:ObjectProperty ; + rdfs:label "upstream resource ids" ; rdfs:domain biolink:RetrievalSource ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:node_property ; @@ -5388,11 +5474,11 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -5717,13 +5803,13 @@ biolink:FDA_approval_status a owl:ObjectProperty ; biolink:FrequencyQuantifier a owl:Class ; rdfs:label "frequency quantifier" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -5942,11 +6028,11 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation ; @@ -6740,10 +6826,6 @@ biolink:GeneExpressionMixin a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LifeStage ; @@ -6752,27 +6834,31 @@ biolink:GeneExpressionMixin a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." . biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:Disease ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; @@ -6788,11 +6874,11 @@ biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; @@ -6854,33 +6940,35 @@ biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:exact_match ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalContextQualifierEnum ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:broad_match ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onClass biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -6888,51 +6976,49 @@ biolink:PredicateMapping a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_context_qualifier ], + owl:onClass biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ] ; + owl:onProperty biolink:object_aspect_qualifier ] ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." . biolink:Protein a owl:Class ; @@ -6950,23 +7036,6 @@ biolink:Protein a owl:Class ; skos:narrowMatch STY:T126, STY:T192 . -biolink:RetrievalSource a owl:Class ; - rdfs:label "retrieval source" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:ResourceRoleEnum ; - owl:onProperty biolink:resource_role ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:upstream_resources ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:resource ; - owl:qualifiedCardinality 1 ], - biolink:InformationContentEntity ; - skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." . - biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; @@ -7214,16 +7283,16 @@ biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Dataset ; - owl:onProperty dct:source ], + owl:onClass biolink:DatasetDistribution ; + owl:onProperty dct:distribution ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty pav:version ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DatasetDistribution ; - owl:onProperty dct:distribution ], + owl:onClass biolink:Dataset ; + owl:onProperty dct:source ], biolink:InformationContentEntity ; skos:definition "an item that holds version level information about a dataset." . @@ -7273,13 +7342,13 @@ biolink:PhysicalEntity a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Unit ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_numeric_value ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Unit ; + owl:onProperty biolink:has_unit ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" . @@ -7596,6 +7665,23 @@ biolink:LifeStage a owl:Class ; skos:exactMatch ; skos:narrowMatch HsapDv:0000000 . +biolink:RetrievalSource a owl:Class ; + rdfs:label "retrieval source" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:ResourceRoleEnum ; + owl:onProperty biolink:resource_role ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:upstream_resource_ids ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:resource_id ; + owl:qualifiedCardinality 1 ], + biolink:InformationContentEntity ; + skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." . + biolink:StudyResult a owl:Class ; rdfs:label "study result" ; rdfs:subClassOf biolink:InformationContentEntity ; @@ -7759,19 +7845,19 @@ biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:highest_FDA_approval_status ], + owl:onClass biolink:ChemicalMixture ; + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalMixture ; - owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], + owl:onClass linkml:String ; + owl:onProperty biolink:highest_FDA_approval_status ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -8118,8 +8204,12 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; @@ -8127,19 +8217,15 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], biolink:EntityToFeatureOrDiseaseQualifiersMixin, biolink:FrequencyQuantifier, linkml:mixin . @@ -8147,13 +8233,13 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -8292,8 +8378,12 @@ biolink:participates_in a owl:ObjectProperty ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; @@ -8303,19 +8393,15 @@ biolink:Entity a owl:Class ; owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NarrativeText ; - owl:onProperty dct:description ], + owl:onClass biolink:IriType ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ], + owl:onClass biolink:NarrativeText ; + owl:onProperty dct:description ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ] ; + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . biolink:InformationResource a owl:Class ; @@ -8461,37 +8547,37 @@ biolink:EntityToDiseaseAssociationMixin a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:StrandEnum ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:StrandEnum ; owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:start_interbase_coordinate ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:PhaseEnum ; owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:StrandEnum ; - owl:onProperty biolink:genome_build ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:start_interbase_coordinate ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -8581,12 +8667,12 @@ biolink:MolecularActivity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -8600,6 +8686,13 @@ biolink:MolecularActivity a owl:Class ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:affiliation ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:address ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], @@ -8607,13 +8700,6 @@ biolink:Agent a owl:Class ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:affiliation ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:address ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -8629,14 +8715,14 @@ biolink:Agent a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; - owl:onProperty biolink:enabled_by ], + owl:allValuesFrom biolink:Occurrent ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:Occurrent ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Occurrent ; - owl:onProperty biolink:has_output ], + owl:allValuesFrom biolink:PhysicalEntity ; + owl:onProperty biolink:enabled_by ], biolink:BiologicalEntity, biolink:Occurrent, biolink:OntologyClass ; @@ -8680,12 +8766,12 @@ biolink:timepoint a owl:ObjectProperty ; biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], biolink:GenomicEntity, biolink:MolecularEntity, biolink:OntologyClass, @@ -8798,11 +8884,11 @@ biolink:InformationContentEntity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:format ], + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:license ], + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -8833,33 +8919,33 @@ biolink:InformationContentEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:mesh_terms ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], + [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:mesh_terms ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:summary ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty dct:type ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:pages ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:summary ], biolink:InformationContentEntity ; skos:definition "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses." ; skos:exactMatch IAO:0000311 ; @@ -8869,20 +8955,20 @@ biolink:Publication a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], biolink:NamedThing, biolink:OntologyClass ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; @@ -8926,16 +9012,16 @@ biolink:AnatomicalEntity a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -8955,21 +9041,21 @@ biolink:ChemicalEntity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalRole ; owl:onProperty biolink:has_chemical_role ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Boolean ; owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; - owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalEntity ; owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:ChemicalEntityOrProteinOrPolypeptide, biolink:ChemicalOrDrugOrTreatment, @@ -8999,14 +9085,14 @@ biolink:Gene a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:LabelType ; owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:symbol ], biolink:BiologicalEntity, biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:GeneOrGeneProduct, @@ -9074,17 +9160,6 @@ biolink:OntologyClass a owl:Class ; "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; linkml:examples "Example(value='UBERON:0000955', description=\"the class 'brain' from the Uberon anatomy ontology\")" . -biolink:association_slot a owl:ObjectProperty ; - rdfs:label "association slot" ; - rdfs:domain biolink:Association ; - rdfs:range linkml:String ; - skos:altLabel "edge property", - "edge qualifier", - "node qualifier", - "statement property", - "statement qualifier" ; - skos:definition "any slot that relates an association to another entity" . - biolink:node_property a owl:ObjectProperty ; rdfs:label "node property" ; rdfs:domain biolink:NamedThing ; @@ -9101,6 +9176,17 @@ rdf:object a owl:ObjectProperty ; rdf:object, owl:annotatedTarget . +biolink:association_slot a owl:ObjectProperty ; + rdfs:label "association slot" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:String ; + skos:altLabel "edge property", + "edge qualifier", + "node qualifier", + "statement property", + "statement qualifier" ; + skos:definition "any slot that relates an association to another entity" . + rdf:subject a owl:ObjectProperty ; rdfs:label "subject" ; rdfs:domain biolink:Association ; @@ -9123,63 +9209,100 @@ biolink:related_to_at_instance_level a owl:ObjectProperty, biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:original_object ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:InformationResource ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:negated ], + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:original_subject ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:allValuesFrom biolink:InformationResource ; owl:onProperty biolink:aggregator_knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:subject_closure ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:InformationResource ; owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:object_label_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:original_predicate ], + owl:onClass linkml:String ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty biolink:negated ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:original_object ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, diff --git a/biolink-model.proto b/biolink-model.proto index 8c586926bf..a5d9cfad44 100644 --- a/biolink-model.proto +++ b/biolink-model.proto @@ -78,6 +78,17 @@ message AnatomicalEntityToAnatomicalEntityOntogenicAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 anatomicalEntity subject = 0 @@ -103,6 +114,17 @@ message AnatomicalEntityToAnatomicalEntityPartOfAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 anatomicalEntity subject = 0 @@ -157,6 +179,17 @@ message Association string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 } @@ -212,6 +245,17 @@ message BehaviorToBehavioralFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 behavior subject = 0 @@ -406,6 +450,17 @@ message CaseToPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 frequencyValue frequencyQualifier = 0 @@ -463,6 +518,17 @@ message CellLineAsAModelOfDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 cellLine subject = 0 @@ -491,6 +557,17 @@ message CellLineToDiseaseOrPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 diseaseOrPhenotypicFeature subject = 0 @@ -541,6 +618,17 @@ message ChemicalAffectsGeneAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 chemicalOrGeneOrGeneProductFormOrVariantEnum subjectFormOrVariantQualifier = 0 @@ -598,6 +686,17 @@ message ChemicalEntityAssessesNamedThingAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 chemicalEntity subject = 0 @@ -623,6 +722,17 @@ message ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 directionQualifierEnum objectDirectionQualifier = 0 @@ -666,6 +776,17 @@ message ChemicalGeneInteractionAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 chemicalOrGeneOrGeneProductFormOrVariantEnum subjectFormOrVariantQualifier = 0 @@ -723,6 +844,17 @@ message ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 fDAIDAAdverseEventEnum fDAAdverseEventLevel = 0 @@ -749,6 +881,17 @@ message ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 fDAIDAAdverseEventEnum fDAAdverseEventLevel = 0 @@ -791,6 +934,17 @@ message ChemicalToChemicalAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 chemicalEntity object = 0 @@ -821,6 +975,17 @@ message ChemicalToChemicalDerivationAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 repeated macromolecularMachineMixin catalystQualifier = 0 @@ -849,6 +1014,17 @@ message ChemicalToDiseaseOrPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 diseaseOrPhenotypicFeature object = 0 @@ -873,6 +1049,17 @@ message ChemicalToPathwayAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 chemicalEntity subject = 0 @@ -1151,6 +1338,17 @@ message ContributorAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 informationContentEntity subject = 0 @@ -1310,6 +1508,17 @@ message DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -1336,6 +1545,17 @@ message DiseaseOrPhenotypicFeatureToLocationAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 anatomicalEntity object = 0 @@ -1362,6 +1582,17 @@ message DiseaseToExposureEventAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 } @@ -1385,6 +1616,17 @@ message DiseaseToPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 disease subject = 0 @@ -1458,6 +1700,17 @@ message DrugToGeneAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 geneOrGeneProduct object = 0 @@ -1497,6 +1750,17 @@ message DruggableGeneToDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 disease object = 0 @@ -1528,6 +1792,17 @@ message EntityToDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 fDAApprovalStatusEnum fDAApprovalStatus = 0 @@ -1553,6 +1828,17 @@ message EntityToPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 fDAApprovalStatusEnum fDAApprovalStatus = 0 @@ -1686,6 +1972,17 @@ message ExonToTranscriptRelationship string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 exon subject = 0 @@ -1713,6 +2010,17 @@ message ExposureEventToOutcomeAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 populationOfIndividualOrganisms populationContextQualifier = 0 @@ -1739,6 +2047,17 @@ message ExposureEventToPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 exposureEvent subject = 0 @@ -1810,6 +2129,17 @@ message FunctionalAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 macromolecularMachineMixin subject = 0 @@ -1851,6 +2181,17 @@ message GeneAsAModelOfDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 disease object = 0 @@ -1892,6 +2233,17 @@ message GeneHasVariantThatContributesToDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 frequencyValue frequencyQualifier = 0 @@ -1921,6 +2273,17 @@ message GeneToDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 geneOrGeneProduct subject = 0 @@ -1948,6 +2311,17 @@ message GeneToExpressionSiteAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 lifeStage stageQualifier = 0 @@ -1975,6 +2349,17 @@ message GeneToGeneCoexpressionAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 geneOrGeneProduct subject = 0 @@ -2004,6 +2389,17 @@ message GeneToGeneFamilyAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 gene subject = 0 @@ -2029,6 +2425,17 @@ message GeneToGeneHomologyAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 geneOrGeneProduct subject = 0 @@ -2054,6 +2461,17 @@ message GeneToGeneProductRelationship string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 gene subject = 0 @@ -2079,6 +2497,17 @@ message GeneToGoTermAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 gene subject = 0 @@ -2104,6 +2533,17 @@ message GeneToPathwayAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 geneOrGeneProduct subject = 0 @@ -2128,6 +2568,17 @@ message GeneToPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 geneOrGeneProduct subject = 0 @@ -2209,6 +2660,17 @@ message GenomicSequenceLocalization string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 integer startInterbaseCoordinate = 0 @@ -2254,6 +2716,17 @@ message GenotypeAsAModelOfDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -2281,6 +2754,17 @@ message GenotypeToDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 namedThing subject = 0 @@ -2309,6 +2793,17 @@ message GenotypeToGeneAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -2334,6 +2829,17 @@ message GenotypeToGenotypePartAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -2360,6 +2866,17 @@ message GenotypeToPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -2392,6 +2909,17 @@ message GenotypeToVariantAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -2535,6 +3063,17 @@ message InformationContentEntityToNamedThingAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 namedThing subject = 0 @@ -2606,6 +3145,17 @@ message MacromolecularMachineToBiologicalProcessAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 macromolecularMachineMixin subject = 0 @@ -2631,6 +3181,17 @@ message MacromolecularMachineToCellularComponentAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 macromolecularMachineMixin subject = 0 @@ -2656,6 +3217,17 @@ message MacromolecularMachineToMolecularActivityAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 macromolecularMachineMixin subject = 0 @@ -2693,6 +3265,17 @@ message MaterialSampleDerivationAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 materialSample subject = 0 @@ -2721,6 +3304,17 @@ message MaterialSampleToDiseaseOrPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 } @@ -2782,6 +3376,17 @@ message MolecularActivityToChemicalEntityAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 molecularActivity subject = 0 @@ -2807,6 +3412,17 @@ message MolecularActivityToMolecularActivityAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 molecularActivity subject = 0 @@ -2831,6 +3447,17 @@ message MolecularActivityToPathwayAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 molecularActivity subject = 0 @@ -2911,6 +3538,17 @@ message NamedThingAssociatedWithLikelihoodOfNamedThingAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -3073,6 +3711,17 @@ message OrganismTaxonToOrganismTaxonInteraction string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 string associatedEnvironmentalContext = 0 @@ -3099,6 +3748,17 @@ message OrganismTaxonToOrganismTaxonSpecialization string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 organismTaxon subject = 0 @@ -3124,6 +3784,17 @@ message OrganismToOrganismAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 individualOrganism subject = 0 @@ -3149,6 +3820,17 @@ message OrganismalEntityAsAModelOfDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 organismalEntity subject = 0 @@ -3175,6 +3857,17 @@ message PairwiseGeneToGeneInteraction string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 geneOrGeneProduct subject = 0 @@ -3199,6 +3892,17 @@ message PairwiseMolecularInteraction string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 ontologyClass interactingMoleculesCategory = 0 @@ -3436,6 +4140,17 @@ message PopulationToPopulationAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 populationOfIndividualOrganisms subject = 0 @@ -3624,6 +4339,17 @@ message ReactionToCatalystAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 integer stoichiometry = 0 @@ -3651,6 +4377,17 @@ message ReactionToParticipantAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 chemicalEntity object = 0 @@ -3726,9 +4463,9 @@ message RetrievalSource string rights = 0 string format = 0 date creationDate = 0 - uriorcurie resource = 0 + uriorcurie resourceId = 0 resourceRoleEnum resourceRole = 0 - uriorcurie upstreamResources = 0 + uriorcurie upstreamResourceIds = 0 repeated uriorcurie xref = 0 } message RNAProduct @@ -3796,6 +4533,17 @@ message SequenceAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 } @@ -3819,6 +4567,17 @@ message SequenceFeatureRelationship string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 nucleicAcidEntity subject = 0 @@ -4035,6 +4794,17 @@ message TaxonToTaxonAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 organismTaxon subject = 0 @@ -4103,6 +4873,17 @@ message TranscriptToGeneRelationship string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 transcript subject = 0 @@ -4158,6 +4939,17 @@ message VariantAsAModelOfDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 predicateType predicate = 0 @@ -4185,6 +4977,17 @@ message VariantToDiseaseAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 namedThing subject = 0 @@ -4214,6 +5017,17 @@ message VariantToGeneAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 gene object = 0 @@ -4239,6 +5053,17 @@ message VariantToGeneExpressionAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 gene object = 0 @@ -4268,6 +5093,17 @@ message VariantToPhenotypicFeatureAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 sequenceVariant subject = 0 @@ -4300,6 +5136,17 @@ message VariantToPopulationAssociation string originalSubject = 0 uriorcurie originalPredicate = 0 string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 sequenceVariant subject = 0 diff --git a/biolink-model.shacl.ttl b/biolink-model.shacl.ttl index 80f8e31a4f..50b0687d95 100644 --- a/biolink-model.shacl.ttl +++ b/biolink-model.shacl.ttl @@ -13,28 +13,34 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path dct:description ], [ sh:order 7 ; sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -44,68 +50,62 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ] ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; sh:closed true ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path dct:description ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], - [ sh:order 5 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ] ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -117,18 +117,27 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -138,61 +147,57 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ] ; + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:order 20 ; - sh:path biolink:has_attribute ], + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; @@ -203,205 +208,285 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:iri ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ] ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:object_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 31 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:AnatomicalEntity ; sh:description "the whole" ; sh:maxCount 1 ; @@ -409,51 +494,80 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:AnatomicalEntity ; sh:description "the part" ; sh:maxCount 1 ; @@ -461,24 +575,51 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ] ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . biolink:Annotation a sh:NodeShape ; @@ -490,61 +631,48 @@ biolink:Annotation a sh:NodeShape ; biolink:Article a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "keywords tagging a publication" ; + sh:property [ sh:description "keywords tagging a publication" ; sh:order 7 ; sh:path biolink:keywords ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 9 ; - sh:path biolink:xref ], [ sh:description "page number of source referenced for statement or publication" ; sh:order 5 ; sh:path biolink:pages ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:issue ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:has_attribute ], + [ sh:order 18 ; + sh:path rdf:type ], [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:volume ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ], [ sh:description "mesh terms tagging a publication" ; sh:order 8 ; sh:path biolink:mesh_terms ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:rights ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -554,16 +682,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 20 ; sh:path dct:description ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:order 4 ; sh:path biolink:authors ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 19 ; @@ -571,6 +692,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:maxCount 1 ; sh:order 10 ; sh:path biolink:license ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:summary ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:order 1 ; @@ -581,92 +722,127 @@ biolink:Association a sh:NodeShape ; sh:closed true ; sh:description "A typed association between two entities, supported by evidence" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 17 ; - sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -674,130 +850,130 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ] ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:Association . biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:has_percentage ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:has_count ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:frequency_qualifier ], + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 12 ; + sh:path biolink:original_subject ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:sex_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:severity_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:has_total ], + sh:order 31 ; + sh:path dct:description ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 20 ; - sh:path dct:description ], + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], [ sh:class biolink:BehavioralFeature ; sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; @@ -805,16 +981,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], [ sh:class biolink:Behavior ; sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; @@ -822,41 +1024,57 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:has_quotient ] ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; sh:closed true ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; @@ -865,11 +1083,26 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; @@ -879,6 +1112,13 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -888,14 +1128,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -907,13 +1142,25 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -923,71 +1170,45 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 2 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + sh:path dct:description ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:enabled_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:class biolink:Occurrent ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path biolink:has_input ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + [ sh:class biolink:Occurrent ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path biolink:has_output ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -997,34 +1218,49 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:order 9 ; sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:Occurrent ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path biolink:has_output ] ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:enabled_by ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:BioticExposure a sh:NodeShape ; sh:closed true ; sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; @@ -1036,8 +1272,10 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:order 10 ; - sh:path rdf:type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -1045,15 +1283,15 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], @@ -1062,22 +1300,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -1089,35 +1324,20 @@ biolink:Book a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], - [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + sh:property [ sh:description "page number of source referenced for statement or publication" ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 15 ; + sh:path rdfs:label ], [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:order 0 ; sh:path biolink:authors ], @@ -1125,15 +1345,32 @@ biolink:Book a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:creation_date ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "page number of source referenced for statement or publication" ; - sh:order 1 ; - sh:path biolink:pages ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1143,16 +1380,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -1163,22 +1398,72 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:creation_date ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ], + [ sh:description "chapter of a book" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:chapter ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], + [ sh:description "page number of source referenced for statement or publication" ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:format ], + [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:description "keywords tagging a publication" ; + sh:order 6 ; + sh:path biolink:keywords ], [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:volume ], + [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 13 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:format ], + sh:order 10 ; + sh:path biolink:rights ], + [ sh:order 17 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1188,62 +1473,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 16 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], [ sh:description "mesh terms tagging a publication" ; sh:order 7 ; sh:path biolink:mesh_terms ], - [ sh:description "chapter of a book" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:chapter ], - [ sh:description "page number of source referenced for statement or publication" ; - sh:order 4 ; - sh:path biolink:pages ], [ sh:maxCount 1 ; sh:order 9 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:rights ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 13 ; - sh:path biolink:provided_by ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:creation_date ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ] ; + sh:path biolink:license ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; @@ -1256,163 +1491,206 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:property [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "number of things with a particular property" ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:has_count ], - [ sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:has_quotient ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:severity_qualifier ], + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:order 18 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:order 29 ; sh:path rdf:type ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 16 ; + sh:path biolink:object_category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Case ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:has_percentage ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 31 ; sh:path dct:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 23 ; + sh:order 34 ; sh:path biolink:has_total ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Case ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ] ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1427,176 +1705,228 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + [ sh:order 6 ; + sh:path rdf:type ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:property [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 30 ; + sh:path dct:description ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 33 ; sh:path biolink:onset_qualifier ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:order 28 ; + sh:path rdf:type ] ; sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -1604,77 +1934,123 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:order 17 ; - sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 30 ; + sh:path dct:description ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ] ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; @@ -1687,13 +2063,16 @@ biolink:CellularOrganism a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1703,26 +2082,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 2 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -1737,676 +2113,491 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_evidence ], + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:original_predicate ], - [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:id ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path rdf:predicate ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "a point in time" ; + sh:order 18 ; + sh:path biolink:publications ], + [ sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:timepoint ], + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 15 ; - sh:path rdf:object ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:order 30 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:publications ], + sh:order 14 ; + sh:path rdf:predicate ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 29 ; + sh:order 40 ; sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:original_object ], [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_evidence ], [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:order 28 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path rdfs:label ], - [ sh:in ( "metabolite" ) ; + sh:path biolink:object_category ], + [ sh:order 41 ; + sh:path rdf:type ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 25 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 24 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path dct:description ], + sh:order 27 ; + sh:path biolink:subject_category ], [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 38 ; + sh:path biolink:id ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 44 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 23 ; + sh:path biolink:timepoint ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 16 ; sh:path biolink:negated ], - [ sh:description "a point in time" ; + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_closure ], [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 21 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:subject_label_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 39 ; sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:object_category_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 43 ; + sh:path dct:description ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 13 ; sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:qualifiers ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 26 ; sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 15 ; + sh:path rdf:object ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A regulatory relationship between two genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:order 18 ; - sh:path rdf:type ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:publications ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:description "the direction is always from regulator to regulated" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; + sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:has_evidence ], + sh:path biolink:knowledge_source ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "a point in time" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . - -biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; - sh:closed true ; - sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . - -biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a chemical entity and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . + sh:order 30 ; + sh:path dct:description ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . -biolink:ChemicalExposure a sh:NodeShape ; +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A chemical exposure is an intake of a particular chemical entity." ; + sh:description "A regulatory relationship between two genes" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 20 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:id ], + sh:path biolink:publications ], [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 1 ; + sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:ChemicalExposure . - -biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:order 25 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:path biolink:has_evidence ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 22 ; + sh:order 26 ; sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 10 ; - sh:path rdf:object ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_part_qualifier ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], - [ sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], + sh:path biolink:negated ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 24 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path dct:description ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:negated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 26 ; + sh:order 30 ; sh:path rdfs:label ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ] ; - sh:targetClass biolink:ChemicalGeneInteractionAssociation . - -biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalOrDrugOrTreatment . - -biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; + [ sh:description "the direction is always from regulator to regulated" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2414,1181 +2605,1313 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 27 ; + sh:path biolink:iri ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + +biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . + +biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a chemical entity and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . + +biolink:ChemicalExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical exposure is an intake of a particular chemical entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 6 ; - sh:path biolink:publications ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 3 ; + sh:path biolink:has_attribute_type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:path biolink:timepoint ], + [ sh:description "Alternate CURIEs for a thing" ; sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 11 ; sh:path dct:description ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + sh:targetClass biolink:ChemicalExposure . -biolink:ChemicalToChemicalAssociation a sh:NodeShape ; +biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; + sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path rdf:subject ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:path biolink:object_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 12 ; sh:path biolink:qualifiers ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 38 ; sh:path dct:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path rdf:predicate ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 10 ; + sh:path rdf:object ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:order 36 ; + sh:path rdf:type ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:ChemicalToChemicalAssociation . - -biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description """A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: - IF - R has-input C1 AND - R has-output C2 AND - R enabled-by P AND - R type Reaction - THEN - C1 derives-into C2 <>""" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:in ( "metabolite" ) ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 13 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_part_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 35 ; sh:path biolink:category ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 33 ; sh:path biolink:id ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:ChemicalGeneInteractionAssociation . -biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; sh:closed true ; - sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:targetClass biolink:ChemicalOrDrugOrTreatment . + +biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 6 ; sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 0 ; + sh:order 1 ; sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:order 17 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a chemical entity and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalToEntityAssociationMixin . + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . -biolink:ChemicalToPathwayAssociation a sh:NodeShape ; +biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:description "An interaction between a chemical entity and a biological process or pathway." ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:publications ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 31 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 30 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:path rdf:predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ChemicalToPathwayAssociation . + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . -biolink:ChiSquaredAnalysisResult a sh:NodeShape ; +biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A result of a chi squared analysis." ; + sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "Alternate CURIEs for a thing" ; + sh:property [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 30 ; sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ChiSquaredAnalysisResult . - -biolink:ClinicalCourse a sh:NodeShape ; - sh:closed true ; - sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ClinicalCourse . + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:order 28 ; + sh:path rdf:type ] ; + sh:targetClass biolink:ChemicalToChemicalAssociation . -biolink:ClinicalEntity a sh:NodeShape ; +biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:closed true ; - sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; + sh:description """A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: + IF + R has-input C1 AND + R has-output C2 AND + R enabled-by P AND + R type Reaction + THEN + C1 derives-into C2 <>""" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 27 ; sh:path biolink:iri ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 31 ; sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ClinicalEntity . - -biolink:ClinicalFinding a sh:NodeShape ; - sh:closed true ; - sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:negated ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 30 ; sh:path rdfs:label ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:ClinicalFinding . - -biolink:ClinicalIntervention a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:iri ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path rdfs:label ], + sh:path biolink:publications ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; + sh:order 26 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ClinicalIntervention . + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . -biolink:ClinicalMeasurement a sh:NodeShape ; +biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; + sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:path rdf:object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:path biolink:negated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 30 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:ClinicalMeasurement . - -biolink:ClinicalModifier a sh:NodeShape ; - sh:closed true ; - sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:path biolink:timepoint ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:ClinicalModifier . - -biolink:ClinicalTrial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ClinicalTrial . + sh:order 26 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . -biolink:CodingSequence a sh:NodeShape ; +biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:closed true ; + sh:description "An interaction between a chemical entity and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:targetClass biolink:ChemicalToEntityAssociationMixin . + +biolink:ChemicalToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a chemical entity and a biological process or pathway." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 30 ; sh:path dct:description ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:is_metabolite ], + sh:path biolink:negated ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:path biolink:qualifiers ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:id ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:CodingSequence . + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ChemicalToPathwayAssociation . -biolink:Cohort a sh:NodeShape ; +biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; - sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; + sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; - sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; + sh:order 11 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Cohort . - -biolink:CommonDataElement a sh:NodeShape ; - sh:closed true ; - sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], @@ -3597,30 +3920,48 @@ biolink:CommonDataElement a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:ChiSquaredAnalysisResult . + +biolink:ClinicalCourse a sh:NodeShape ; + sh:closed true ; + sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:license ], + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:order 9 ; - sh:path rdf:type ], + sh:path biolink:has_qualitative_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3630,179 +3971,126 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:CommonDataElement . - -biolink:ComplexChemicalExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:ClinicalCourse . + +biolink:ClinicalEntity a sh:NodeShape ; + sh:closed true ; + sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 6 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 8 ; + sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:order 2 ; sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:ComplexChemicalExposure . + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ClinicalEntity . -biolink:ComplexMolecularMixture a sh:NodeShape ; +biolink:ClinicalFinding a sh:NodeShape ; sh:closed true ; - sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; + sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:order 8 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 3 ; sh:path biolink:id ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate CURIEs for a thing" ; sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 13 ; + sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; - sh:maxCount 1 ; + [ sh:class biolink:ClinicalAttribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ] ; - sh:targetClass biolink:ComplexMolecularMixture . + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ClinicalFinding . -biolink:ConceptCountAnalysisResult a sh:NodeShape ; +biolink:ClinicalIntervention a sh:NodeShape ; sh:closed true ; - sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:order 0 ; sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3810,73 +4098,74 @@ biolink:ConceptCountAnalysisResult a sh:NodeShape ; This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 8 ; + sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:order 2 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 6 ; sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; - sh:targetClass biolink:ConceptCountAnalysisResult . + sh:order 8 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ClinicalIntervention . -biolink:ConfidenceLevel a sh:NodeShape ; +biolink:ClinicalMeasurement a sh:NodeShape ; sh:closed true ; - sh:description "Level of confidence in a statement" ; + sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; + sh:order 7 ; sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:license ], + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3886,488 +4175,618 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:ConfidenceLevel . + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; + sh:targetClass biolink:ClinicalMeasurement . -biolink:ContributorAssociation a sh:NodeShape ; +biolink:ClinicalModifier a sh:NodeShape ; sh:closed true ; - sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; + sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 10 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationContentEntity ; - sh:description "information content entity which an agent has helped realise" ; - sh:maxCount 1 ; sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; + sh:targetClass biolink:ClinicalModifier . + +biolink:ClinicalTrial a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; + sh:order 7 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:ContributorAssociation . - -biolink:DatasetSummary a sh:NodeShape ; - sh:closed true ; - sh:description "an item that holds summary level information about a dataset." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; + sh:order 1 ; sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:source_web_page ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:format ], + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 10 ; + sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:order 11 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:rights ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path schema:logo ] ; - sh:targetClass biolink:DatasetSummary . + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ClinicalTrial . -biolink:DatasetVersion a sh:NodeShape ; +biolink:CodingSequence a sh:NodeShape ; sh:closed true ; - sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:format ], + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; + sh:order 2 ; sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; + sh:order 10 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path pav:version ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:rights ], - [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path dct:source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:order 12 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:order 13 ; sh:path rdf:type ], - [ sh:maxCount 1 ; + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:is_metabolite ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 14 ; - sh:path dct:description ], + sh:path rdfs:label ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 11 ; + sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:DatasetVersion . + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ] ; + sh:targetClass biolink:CodingSequence . -biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; +biolink:Cohort a sh:NodeShape ; sh:closed true ; - sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; + sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; + sh:order 7 ; sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 9 ; + sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 8 ; sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; + sh:targetClass biolink:Cohort . + +biolink:CommonDataElement a sh:NodeShape ; + sh:closed true ; + sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; + sh:order 5 ; sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; + sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "a point in time" ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . - -biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureOutcome . - -biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ] ; + sh:targetClass biolink:CommonDataElement . -biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; +biolink:ComplexChemicalExposure a sh:NodeShape ; sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; + sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 11 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:targetClass biolink:ComplexChemicalExposure . + +biolink:ComplexMolecularMixture a sh:NodeShape ; + sh:closed true ; + sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:order 14 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:has_chemical_role ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 16 ; sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 15 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + sh:path biolink:iri ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ComplexMolecularMixture . -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; +biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; + sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; - sh:path biolink:qualifiers ], + sh:path biolink:provided_by ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 11 ; + sh:path dct:description ] ; + sh:targetClass biolink:ConceptCountAnalysisResult . + +biolink:ConfidenceLevel a sh:NodeShape ; + sh:closed true ; + sh:description "Level of confidence in a statement" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 6 ; - sh:path biolink:has_evidence ], + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ] ; + sh:targetClass biolink:ConfidenceLevel . + +biolink:ContributorAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; @@ -4376,24 +4795,27 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:category ], + sh:path biolink:subject_closure ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; @@ -4401,312 +4823,246 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:primary_knowledge_source ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 29 ; sh:path rdfs:label ], + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . - -biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:DiseaseToEntityAssociationMixin . - -biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and a disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:ContributorAssociation . + +biolink:DatasetSummary a sh:NodeShape ; + sh:closed true ; + sh:description "an item that holds summary level information about a dataset." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:logo ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 9 ; sh:path biolink:iri ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:rights ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:creation_date ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 8 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:source_web_page ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 12 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:license ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . + sh:order 14 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:DatasetSummary . -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:DatasetVersion a sh:NodeShape ; sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:property [ sh:order 12 ; + sh:path rdf:type ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:has_total ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:rights ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:severity_qualifier ], + sh:order 14 ; + sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; + sh:order 10 ; sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path pav:version ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:DatasetDistribution ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:predicate ], + sh:path dct:distribution ], + [ sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:format ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Dataset ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path dct:source ], + [ sh:maxCount 1 ; sh:order 3 ; - sh:path rdf:object ], - [ sh:order 18 ; + sh:path biolink:license ] ; + sh:targetClass biolink:DatasetVersion . + +biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:order 10 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:negated ], - [ sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:has_count ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:onset_qualifier ] ; - sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . - -biolink:DrugExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A drug exposure is an intake of a particular drug." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:path biolink:has_qualitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4716,32 +5072,16 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 10 ; - sh:path rdf:type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:path biolink:has_quantitative_value ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; @@ -4754,1710 +5094,3198 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "Alternate CURIEs for a thing" ; sh:order 8 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:DrugExposure . + sh:order 2 ; + sh:path biolink:has_attribute_type ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . -biolink:DrugToEntityAssociationMixin a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; sh:closed true ; - sh:description "An interaction between a drug and another entity" ; + sh:description "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:DrugToEntityAssociationMixin . + sh:targetClass biolink:DiseaseOrPhenotypicFeatureOutcome . -biolink:DrugToGeneAssociation a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed true ; - sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + +biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:Drug ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:DrugToGeneAssociation . - -biolink:DrugToGeneInteractionExposure a sh:NodeShape ; - sh:closed true ; - sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:timepoint ], + sh:path rdf:predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; + sh:order 25 ; sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ] ; - sh:targetClass biolink:DrugToGeneInteractionExposure . + sh:order 24 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . -biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:closed true ; + sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:onset_qualifier ], + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:DiseaseToEntityAssociationMixin . + +biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and a disease." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ] ; - sh:targetClass biolink:DruggableGeneToDiseaseAssociation . - -biolink:Entity a sh:NodeShape ; - sh:closed true ; - sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 31 ; sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 2 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:order 3 ; - sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path dct:description ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Entity . - -biolink:EntityToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:path biolink:object_category_closure ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Disease ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_approval_status ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:order 29 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ] ; - sh:targetClass biolink:EntityToDiseaseAssociation . - -biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:description "mixin class for any association whose object (target node) is a disease" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Onset ; + sh:order 31 ; + sh:path dct:description ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; + sh:order 38 ; sh:path biolink:onset_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 37 ; sh:path biolink:severity_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:EntityToDiseaseAssociationMixin . - -biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . - -biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:description "An association between some entity and an exposure event." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:EntityToExposureEventAssociationMixin . - -biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; - sh:closed true ; - sh:description "Qualifiers for entity to disease or phenotype associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:onset_qualifier ], + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 2 ; + sh:order 39 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:severity_qualifier ] ; - sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . - -biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:description "An association between some entity and an outcome" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:EntityToOutcomeAssociationMixin . - -biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_approval_status ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . - -biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:severity_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:onset_qualifier ] ; - sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . + sh:order 8 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . -biolink:EnvironmentalExposure a sh:NodeShape ; +biolink:DrugExposure a sh:NodeShape ; sh:closed true ; - sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; + sh:description "A drug exposure is an intake of a particular drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:order 10 ; + sh:property [ sh:order 10 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a point in time" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:EnvironmentalExposure . - -biolink:EnvironmentalFeature a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:EnvironmentalFeature . + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:DrugExposure . -biolink:EnvironmentalFoodContaminant a sh:NodeShape ; +biolink:DrugToEntityAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a drug and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:DrugToEntityAssociationMixin . + +biolink:DrugToGeneAssociation a sh:NodeShape ; sh:closed true ; + sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; - sh:path dct:description ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:path biolink:original_predicate ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; + sh:order 25 ; sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:description "" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:EnvironmentalFoodContaminant . - -biolink:EnvironmentalProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; + sh:path biolink:knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path rdfs:label ], + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Drug ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:order 5 ; - sh:path rdf:type ] ; - sh:targetClass biolink:EnvironmentalProcess . + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:DrugToGeneAssociation . -biolink:EpidemiologicalOutcome a sh:NodeShape ; +biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:closed true ; - sh:description "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; + sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:EpidemiologicalOutcome . - -biolink:EpigenomicEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:EpigenomicEntity . - -biolink:Event a sh:NodeShape ; - sh:closed true ; - sh:description "Something that happens at a given place and time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 9 ; sh:path biolink:xref ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 4 ; + sh:order 10 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Event . + sh:order 7 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:DrugToGeneInteractionExposure . -biolink:ExonToTranscriptRelationship a sh:NodeShape ; +biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:order 17 ; - sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:ExonToTranscriptRelationship . - -biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path dct:description ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:Outcome ; + [ sh:class biolink:Disease ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:iri ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path rdf:subject ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:id ], + sh:path biolink:subject_closure ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 32 ; + sh:path biolink:severity_qualifier ] ; + sh:targetClass biolink:DruggableGeneToDiseaseAssociation . + +biolink:Entity a sh:NodeShape ; + sh:closed true ; + sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 18 ; + sh:order 2 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_predicate ], - [ sh:order 19 ; - sh:path rdf:type ], - [ sh:description "a point in time" ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ] ; - sh:targetClass biolink:ExposureEventToOutcomeAssociation . + sh:order 4 ; + sh:path rdfs:label ], + [ sh:order 3 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Entity . -biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:closed true ; - sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "total number of things in a particular reference set" ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:has_total ], - [ sh:class biolink:PhenotypicFeature ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:description "" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:FDA_approval_status ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:frequency_qualifier ], + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:id ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:has_count ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:has_quotient ], + sh:order 16 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 28 ; sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path rdfs:label ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ] ; - sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . - -biolink:Food a sh:NodeShape ; - sh:closed true ; - sh:description "A substance consumed by a living organism as a source of nutrition" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalMixture ; - sh:description "" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:subject ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path rdfs:label ], + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ] ; + sh:targetClass biolink:EntityToDiseaseAssociation . + +biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:description "mixin class for any association whose object (target node) is a disease" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:severity_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:onset_qualifier ] ; + sh:targetClass biolink:EntityToDiseaseAssociationMixin . + +biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + +biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:description "An association between some entity and an exposure event." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:EntityToExposureEventAssociationMixin . + +biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; + sh:closed true ; + sh:description "Qualifiers for entity to disease or phenotype associations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:severity_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:onset_qualifier ] ; + sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . + +biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:description "An association between some entity and an outcome" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:EntityToOutcomeAssociationMixin . + +biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 26 ; sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_approval_status ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:xref ], + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 27 ; sh:path biolink:iri ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ] ; + sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . + +biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:severity_qualifier ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_total ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_count ] ; + sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . + +biolink:EnvironmentalExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:EnvironmentalExposure . + +biolink:EnvironmentalFeature a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ] ; + sh:targetClass biolink:EnvironmentalFeature . + +biolink:EnvironmentalFoodContaminant a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ] ; + sh:targetClass biolink:EnvironmentalFoodContaminant . + +biolink:EnvironmentalProcess a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path dct:description ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:EnvironmentalProcess . + +biolink:EpidemiologicalOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:EpidemiologicalOutcome . + +biolink:EpigenomicEntity a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:EpigenomicEntity . + +biolink:Event a sh:NodeShape ; + sh:closed true ; + sh:description "Something that happens at a given place and time." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path dct:description ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Event . + +biolink:ExonToTranscriptRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A transcript is formed from multiple exons" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Exon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Transcript ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ExonToTranscriptRelationship . + +biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:object_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:id ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_predicate ], + [ sh:order 30 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:object_closure ], + [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 29 ; + sh:path biolink:category ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path rdfs:label ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path dct:description ] ; + sh:targetClass biolink:ExposureEventToOutcomeAssociation . + +biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . + +biolink:Food a sh:NodeShape ; + sh:closed true ; + sh:description "A substance consumed by a living organism as a source of nutrition" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path dct:description ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ] ; + sh:targetClass biolink:Food . + +biolink:FoodAdditive a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; + sh:targetClass biolink:FoodAdditive . + +biolink:FrequencyQualifierMixin a sh:NodeShape ; + sh:closed true ; + sh:description "Qualifier for frequency type associations" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:frequency_qualifier ] ; + sh:targetClass biolink:FrequencyQualifierMixin . + +biolink:FrequencyQuantifier a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_percentage ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_total ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_count ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_quotient ] ; + sh:targetClass biolink:FrequencyQuantifier . + +biolink:FunctionalAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:FunctionalAssociation . + +biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ] ; - sh:targetClass biolink:Food . - -biolink:FoodAdditive a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 30 ; sh:path dct:description ], - [ sh:description "" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ] ; - sh:targetClass biolink:FoodAdditive . + sh:order 26 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . -biolink:FrequencyQualifierMixin a sh:NodeShape ; +biolink:GeneExpressionMixin a sh:NodeShape ; sh:closed true ; - sh:description "Qualifier for frequency type associations" ; + sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:FrequencyQualifierMixin . - -biolink:FrequencyQuantifier a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "total number of things in a particular reference set" ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_total ], - [ sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_quotient ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:path biolink:stage_qualifier ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_percentage ] ; - sh:targetClass biolink:FrequencyQuantifier . + sh:path biolink:phenotypic_state ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ] ; + sh:targetClass biolink:GeneExpressionMixin . -biolink:FunctionalAssociation a sh:NodeShape ; +biolink:GeneGroupingMixin a sh:NodeShape ; sh:closed true ; - sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; + sh:description "any grouping of multiple genes or gene products" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ] ; + sh:targetClass biolink:GeneGroupingMixin . + +biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 31 ; + sh:path dct:description ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 12 ; sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:maxCount 1 ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path rdf:predicate ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:onset_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ] ; - sh:targetClass biolink:FunctionalAssociation . + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . -biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; +biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:closed true ; + sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:GeneProductIsoformMixin . + +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 33 ; + sh:path biolink:onset_qualifier ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:severity_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; @@ -6469,279 +8297,375 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . - -biolink:GeneExpressionMixin a sh:NodeShape ; - sh:closed true ; - sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ] ; - sh:targetClass biolink:GeneExpressionMixin . - -biolink:GeneGroupingMixin a sh:NodeShape ; - sh:closed true ; - sh:description "any grouping of multiple genes or gene products" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ] ; - sh:targetClass biolink:GeneGroupingMixin . - -biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:onset_qualifier ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:maxCount 1 ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "a point in time" ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToEntityAssociationMixin a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:GeneToEntityAssociationMixin . + +biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:id ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 1 ; + sh:order 2 ; sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 23 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:severity_qualifier ], + sh:order 14 ; + sh:path biolink:original_predicate ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; + sh:order 28 ; sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 15 ; + sh:path biolink:original_object ], + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:stage_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path dct:description ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 17 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_attribute ], + [ sh:order 30 ; + sh:path rdf:type ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "expression relationship" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 29 ; sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . - -biolink:GeneProductIsoformMixin a sh:NodeShape ; - sh:closed true ; - sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 31 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "Alternate CURIEs for a thing" ; + sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:GeneProductIsoformMixin . + sh:path biolink:quantifier_qualifier ] ; + sh:targetClass biolink:GeneToExpressionSiteAssociation . -biolink:GeneToDiseaseAssociation a sh:NodeShape ; +biolink:GeneToGeneAssociation a sh:NodeShape ; sh:closed true ; + sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:onset_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; @@ -6749,733 +8673,687 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:primary_knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToEntityAssociationMixin a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:GeneToEntityAssociationMixin . + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:GeneToGeneAssociation . -biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; +biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:closed true ; - sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; + sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "A measurable quantity for the object of the association" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 33 ; sh:path rdfs:label ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; - sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 21 ; + sh:order 34 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 9 ; + sh:path biolink:publications ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 29 ; sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:description "expression relationship" ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; + sh:order 5 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 18 ; + sh:order 31 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], - [ sh:order 19 ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:order 32 ; sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_subject ], + sh:order 30 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 2 ; + sh:order 4 ; sh:path rdf:subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:GeneToExpressionSiteAssociation . + sh:order 25 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . -biolink:GeneToGeneAssociation a sh:NodeShape ; +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; sh:closed true ; - sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:path biolink:subject_category ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:order 17 ; - sh:path rdf:type ] ; - sh:targetClass biolink:GeneToGeneAssociation . - -biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 30 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 20 ; + sh:order 27 ; sh:path biolink:category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 18 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:order 29 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . + +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "A measurable quantity for the object of the association" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:order 21 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "membership of the gene in the given gene family." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:order 15 ; - sh:path biolink:iri ], + sh:path biolink:object_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "homology relationship type" ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "homology relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; + sh:path biolink:negated ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . - -biolink:GeneToGeneProductRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:order 17 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:order 28 ; sh:path rdf:type ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "a point in time" ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Gene ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -7483,323 +9361,399 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 26 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GeneToGeneProductRelationship . biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 30 ; + sh:path dct:description ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:GeneToGoTermAssociation . biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a gene or gene product and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:order 17 ; - sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:GeneToPathwayAssociation . - -biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:iri ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:onset_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], - [ sh:order 18 ; - sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "a point in time" ; + sh:order 13 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:GeneToPathwayAssociation . + +biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:has_total ], + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path rdfs:label ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:severity_qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 28 ; sh:path biolink:category ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -7807,85 +9761,164 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:maxCount 1 ; - sh:order 24 ; + sh:order 35 ; sh:path biolink:has_quotient ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 22 ; + sh:order 33 ; sh:path biolink:has_count ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:has_percentage ] ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7895,18 +9928,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; @@ -7917,51 +9938,65 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:closed true ; sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 7 ; - sh:path biolink:has_quantitative_value ], + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path rdfs:label ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 7 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:order 13 ; sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 14 ; sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -7969,29 +10004,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_attribute_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ] ; + sh:order 12 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -8007,194 +10028,256 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:closed true ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:property [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:strand ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; + sh:order 34 ; sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 4 ; + sh:path biolink:phase ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:id ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path dct:description ], - [ sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:order 22 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], + sh:order 30 ; + sh:path biolink:id ], [ sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:end_interbase_coordinate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:genome_build ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - sh:in ( "+" "-" "." "?" ) ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ], + [ sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:strand ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:has_attribute ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; + sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 23 ; + sh:order 34 ; sh:path biolink:frequency_qualifier ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -8206,166 +10289,222 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 33 ; sh:path biolink:onset_qualifier ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ] ; sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 33 ; sh:path biolink:onset_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Disease ; sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; @@ -8376,8 +10515,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ] ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; @@ -8389,174 +10551,288 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the relationship type used to connect genotype to gene" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "gene implicated in genotype" ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Gene ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ] ; + sh:order 12 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:GenotypeToGeneAssociation . biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Genotype ; - sh:description "child genotype" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 30 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:description "child genotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; @@ -8566,224 +10842,245 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ] ; + sh:targetClass biolink:GenotypeToGenotypePartAssociation . + +biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:id ], + sh:path biolink:original_object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:GenotypeToGenotypePartAssociation . - -biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:severity_qualifier ], + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:order 29 ; + sh:path rdf:type ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:description "number of things with a particular property" ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:has_count ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; + sh:order 38 ; sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:order 19 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:has_total ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 25 ; + sh:order 36 ; sh:path biolink:has_percentage ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:order 2 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "the relationship type used to connect genotype to gene" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -8791,46 +11088,53 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:SequenceVariant ; sh:description "gene implicated in genotype" ; sh:maxCount 1 ; @@ -8838,34 +11142,91 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ] ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -8873,11 +11234,20 @@ biolink:GenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:order 9 ; sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -8887,67 +11257,64 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:GenotypicSex . + +biolink:GeographicExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:iri ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; - sh:order 2 ; + sh:order 3 ; sh:path biolink:has_quantitative_value ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ] ; - sh:targetClass biolink:GenotypicSex . - -biolink:GeographicExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -8957,27 +11324,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:order 10 ; - sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 1 ; @@ -8988,36 +11338,29 @@ biolink:GeographicLocation a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:order 7 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path dct:description ], [ sh:description "longitude" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:longitude ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:latitude ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9027,10 +11370,17 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "latitude" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:latitude ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; @@ -9041,49 +11391,35 @@ biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:latitude ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path dct:description ], [ sh:description "longitude" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:longitude ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; + [ sh:description "latitude" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path biolink:latitude ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:order 8 ; - sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 4 ; sh:path biolink:xref ], @@ -9091,7 +11427,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; @@ -9101,8 +11451,6 @@ biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9112,27 +11460,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -9140,18 +11474,36 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:in_taxon ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ] ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; sh:closed true ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9161,50 +11513,52 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:has_biological_sequence ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ] ; sh:targetClass biolink:Haplotype . biolink:Hospitalization a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9214,31 +11568,27 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:iri ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ] ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -9251,72 +11601,61 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9324,47 +11663,108 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:order 17 ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:order 28 ; sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9377,129 +11777,164 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "Alternate CURIEs for a thing" ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:MacromolecularComplex . + +biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:MacromolecularComplex . - -biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:id ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9507,29 +11942,79 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ] ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:CellularComponent ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9537,88 +12022,94 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ] ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; @@ -9631,82 +12122,130 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path dct:description ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:path biolink:object_category_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:order 17 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:order 28 ; sh:path rdf:type ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -9719,20 +12258,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ] ; + sh:order 31 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:MappingCollection a sh:NodeShape ; @@ -9750,216 +12288,310 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:path biolink:object_category ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "derivation relationship" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ] ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "derivation relationship" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:MaterialSampleDerivationAssociation . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and a disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 14 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:MaterialSample ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:MaterialSample ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ] ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; @@ -9971,20 +12603,30 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9994,61 +12636,51 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 7 ; sh:path biolink:available_from ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_chemical_role ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_biological_sequence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:order 14 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:is_toxic ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:is_metabolite ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ] ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:max_tolerated_dose ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -10061,62 +12693,121 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10124,26 +12815,75 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 30 ; + sh:path dct:description ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:order 17 ; - sh:path rdf:type ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; @@ -10153,150 +12893,170 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:id ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ] ; + sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + +biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:category ] ; - sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . - -biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10304,167 +13064,180 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:order 18 ; - sh:path rdfs:label ], + sh:path biolink:subject_category_closure ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:MolecularActivityToPathwayAssociation . + +biolink:MolecularMixture a sh:NodeShape ; + sh:closed true ; + sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:MolecularActivityToPathwayAssociation . - -biolink:MolecularMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; sh:path biolink:routes_of_delivery ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 16 ; + sh:path dct:description ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -10477,48 +13250,97 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10526,20 +13348,6 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -10550,86 +13358,65 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . - -biolink:NoncodingRNAProduct a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + +biolink:NoncodingRNAProduct a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 16 ; sh:path dct:description ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; @@ -10638,55 +13425,70 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 9 ; sh:path biolink:is_toxic ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_chemical_role ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:is_metabolite ] ; + sh:path biolink:is_metabolite ], + [ sh:order 14 ; + sh:path rdf:type ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:closed true ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -10695,51 +13497,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:order 7 ; + sh:path rdfs:label ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], @@ -10747,14 +13546,27 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 11 ; - sh:path biolink:synonym ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path biolink:synonym ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10764,50 +13576,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 3 ; - sh:path biolink:xref ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:order 9 ; + sh:property [ sh:order 9 ; sh:path rdf:type ], [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 2 ; + sh:path biolink:format ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], @@ -10820,54 +13619,52 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:OrganismAttribute a sh:NodeShape ; - sh:closed true ; - sh:description "describes a characteristic of an organismal entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:closed true ; + sh:description "describes a characteristic of an organismal entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10877,19 +13674,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; @@ -10901,887 +13721,1263 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "predicate describing the relationship between the taxon and the environment" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "predicate describing the relationship between the taxon and the environment" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ] ; + sh:order 14 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two organism taxon nodes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:path biolink:object_category ], [ sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:associated_environmental_context ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 31 ; + sh:path dct:description ], + [ sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ] ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:closed true ; sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ] ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:order 19 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:iri ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 31 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:OrganismToOrganismAssociation . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Disease ; + sh:property [ sh:class biolink:Disease ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:order 19 ; - sh:path dct:description ], + sh:path biolink:object_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 33 ; sh:path biolink:onset_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ] ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ] ; + sh:order 10 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:PairwiseGeneToGeneInteraction . biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], - [ sh:class biolink:MolecularEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:order 29 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 32 ; sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:MolecularEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 3 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:MolecularEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:PairwiseMolecularInteraction . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -11794,23 +14990,18 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:closed true ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11820,41 +15011,46 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -11867,28 +15063,13 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -11907,6 +15088,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; @@ -11928,20 +15124,29 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Occurrent ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:Occurrent ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11951,32 +15156,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:Occurrent ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Occurrent ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_output ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; @@ -11988,22 +15184,21 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:closed true ; sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12013,19 +15208,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -12035,20 +15217,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 8 ; sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ] ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -12061,36 +15257,24 @@ biolink:Phenomenon a sh:NodeShape ; sh:closed true ; sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 7 ; sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12099,27 +15283,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicQuality a sh:NodeShape ; sh:closed true ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -12127,15 +15314,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; @@ -12144,42 +15347,44 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path dct:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:PhenotypicQuality . biolink:PhenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12189,18 +15394,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 7 ; sh:path biolink:xref ], @@ -12208,20 +15418,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; @@ -12243,75 +15439,76 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:Occurrent ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], [ sh:class biolink:Occurrent ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12321,20 +15518,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], [ sh:order 5 ; sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; @@ -12343,24 +15526,43 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 7 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Polypeptide a sh:NodeShape ; sh:closed true ; sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12370,151 +15572,191 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 9 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Polypeptide . biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path dct:description ], + sh:path biolink:object_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the object of the association" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ] ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12524,108 +15766,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 2 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; - sh:targetClass biolink:PosttranslationalModification . - -biolink:ProcessedMaterial a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:ChemicalMixture ; + sh:order 8 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; + sh:targetClass biolink:PosttranslationalModification . + +biolink:ProcessedMaterial a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -12636,21 +15818,85 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:is_toxic ] ; + sh:path biolink:is_toxic ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; sh:closed true ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], @@ -12658,6 +15904,33 @@ biolink:Protein a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12666,55 +15939,84 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:targetClass biolink:Protein . + +biolink:ProteinDomain a sh:NodeShape ; + sh:closed true ; + sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], [ sh:order 7 ; sh:path rdf:type ] ; - sh:targetClass biolink:Protein . + sh:targetClass biolink:ProteinDomain . -biolink:ProteinDomain a sh:NodeShape ; +biolink:ProteinFamily a sh:NodeShape ; sh:closed true ; - sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:order 7 ; - sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; @@ -12728,11 +16030,11 @@ biolink:ProteinDomain a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12742,52 +16044,36 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ] ; - sh:targetClass biolink:ProteinDomain . + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:order 7 ; + sh:path rdf:type ] ; + sh:targetClass biolink:ProteinFamily . -biolink:ProteinFamily a sh:NodeShape ; +biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:order 7 ; - sh:path rdf:type ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; + sh:order 3 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12797,114 +16083,121 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 1 ; + sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:ProteinFamily . + sh:order 9 ; + sh:path dct:description ] ; + sh:targetClass biolink:ProteinIsoform . -biolink:ProteinIsoform a sh:NodeShape ; +biolink:RNAProduct a sh:NodeShape ; sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 6 ; + sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "" ; sh:maxCount 1 ; sh:order 9 ; - sh:path dct:description ], + sh:path biolink:is_toxic ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:is_metabolite ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ProteinIsoform . - -biolink:RNAProduct a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalRole ; + [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_chemical_role ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:is_metabolite ], + sh:order 16 ; + sh:path dct:description ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ] ; + sh:targetClass biolink:RNAProduct . + +biolink:RNAProductIsoform a sh:NodeShape ; + sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12914,137 +16207,211 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:trade_name ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ] ; - sh:targetClass biolink:RNAProduct . - -biolink:RNAProductIsoform a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 14 ; - sh:path rdf:type ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_chemical_role ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:is_metabolite ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_biological_sequence ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ] ; + sh:targetClass biolink:RNAProductIsoform . + +biolink:ReactionToCatalystAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:order 33 ; + sh:path dct:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:is_metabolite ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:class biolink:MolecularEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:iri ], + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:RNAProductIsoform . - -biolink:ReactionToCatalystAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:order 31 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:knowledge_source ], + [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13052,125 +16419,149 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 5 ; sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:MolecularEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 29 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 34 ; sh:path biolink:has_attribute ], - [ sh:order 20 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 19 ; + sh:order 30 ; sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:reaction_direction ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:order 31 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:MolecularEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13185,89 +16576,35 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:order 20 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 22 ; + sh:order 33 ; sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ] ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; @@ -13277,61 +16614,33 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:property [ sh:description "Alternate CURIEs for a thing" ; sh:order 4 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:order 7 ; - sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ReagentTargetedGene . - -biolink:RegulatoryRegion a sh:NodeShape ; - sh:closed true ; - sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13341,189 +16650,144 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:id ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:ReagentTargetedGene . + +biolink:RegulatoryRegion a sh:NodeShape ; + sh:closed true ; + sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 4 ; - sh:path biolink:xref ], [ sh:order 7 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:RegulatoryRegion . - -biolink:RelationshipQuantifier a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:RelationshipQuantifier . - -biolink:RelationshipType a sh:NodeShape ; - sh:closed true ; - sh:description "An OWL property used as an edge label" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:RelationshipType . - -biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of a relative frequency analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:format ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 8 ; + sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:order 1 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:RelativeFrequencyAnalysisResult . + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:RegulatoryRegion . + +biolink:RelationshipQuantifier a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:RelationshipQuantifier . -biolink:RetrievalSource a sh:NodeShape ; +biolink:RelationshipType a sh:NodeShape ; sh:closed true ; - sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; + sh:description "An OWL property used as an edge label" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:upstream_resources ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:RelationshipType . + +biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; + sh:closed true ; + sh:description "A result of a relative frequency analysis." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 3 ; sh:path biolink:creation_date ], - [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:resource_role ], [ sh:description "Alternate CURIEs for a thing" ; - sh:order 3 ; + sh:order 5 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:license ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:order 12 ; - sh:path rdf:type ], [ sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:rights ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 11 ; + sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:format ], - [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:resource ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:RetrievalSource . + sh:order 11 ; + sh:path dct:description ], + [ sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; sh:closed true ; @@ -13534,39 +16798,39 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13574,116 +16838,127 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:order 17 ; - sh:path rdf:type ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:subject_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:SequenceAssociation . - -biolink:SequenceFeatureRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:SequenceAssociation . + +biolink:SequenceFeatureRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "For example, a particular exon is part of a particular transcript or gene" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13691,167 +16966,297 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:id ], + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path rdfs:label ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:SequenceFeatureRelationship . biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; sh:order 20 ; - sh:path biolink:has_attribute ], + sh:path biolink:subject_namespace ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 7 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; @@ -13862,56 +17267,51 @@ biolink:Serial a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:format ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 0 ; + sh:path biolink:iso_abbreviation ], + [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 13 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:creation_date ], - [ sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], + sh:order 18 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:license ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:summary ], - [ sh:description "page number of source referenced for statement or publication" ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:rights ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:format ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path dct:description ], [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:issue ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 13 ; - sh:path biolink:provided_by ], + [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:order 17 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13921,65 +17321,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 16 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], [ sh:description "mesh terms tagging a publication" ; sh:order 7 ; sh:path biolink:mesh_terms ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:order 3 ; - sh:path biolink:authors ] ; + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "keywords tagging a publication" ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:rights ], + [ sh:description "page number of source referenced for statement or publication" ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:volume ] ; sh:targetClass biolink:Serial . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:is_metabolite ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:trade_name ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13989,25 +17382,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:is_metabolite ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], @@ -14015,137 +17415,142 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ] ; + sh:order 9 ; + sh:path biolink:is_toxic ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_toxic ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:order 11 ; - sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:trade_name ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ] ; + sh:path biolink:is_metabolite ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; sh:closed true ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an entity associated with one or more genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 2 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Gene ; - sh:description "connects an entity associated with one or more genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:order 8 ; sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 1 ; @@ -14160,21 +17565,33 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 8 ; sh:path biolink:xref ], - [ sh:description "a point in time" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14184,44 +17601,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:class biolink:SocioeconomicAttribute ; sh:description "connects any entity to an attribute" ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -14243,6 +17648,14 @@ biolink:Study a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:order 5 ; sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -14254,11 +17667,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; @@ -14267,42 +17680,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ] ; + sh:path biolink:xref ] ; sh:targetClass biolink:Study . biolink:StudyPopulation a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:order 6 ; sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14312,99 +17725,98 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:StudyPopulation . biolink:StudyResult a sh:NodeShape ; sh:closed true ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; sh:closed true ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14414,28 +17826,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], @@ -14443,7 +17833,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -14455,108 +17860,155 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:category ] ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TaxonomicRank a sh:NodeShape ; @@ -14574,58 +18026,58 @@ biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; @@ -14643,76 +18095,58 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is a collection of transcripts" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:id ], + sh:path biolink:subject_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:order 17 ; - sh:path rdf:type ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Transcript ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -14720,67 +18154,114 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:order 7 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -14790,80 +18271,105 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ] ; - sh:targetClass biolink:TranscriptionFactorBindingSite . - -biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; + sh:path biolink:iri ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:TranscriptionFactorBindingSite . + +biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:Disease ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -14876,175 +18382,262 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:order 17 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 33 ; + sh:path biolink:onset_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; - sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; + sh:order 30 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; - sh:path biolink:onset_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:frequency_qualifier ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "E.g. is pathogenic for" ; + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:order 17 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path dct:description ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:subject_closure ], + [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ] ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; @@ -15056,49 +18649,77 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 16 ; + sh:order 27 ; sh:path biolink:category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:SequenceVariant ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -15106,121 +18727,107 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:order 17 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path dct:description ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:VariantToGeneAssociation . - -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path rdf:predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:path biolink:original_object ], + [ sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:order 21 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:VariantToGeneAssociation . + +biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 3 ; + sh:path biolink:phenotypic_state ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 19 ; + sh:order 30 ; sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path rdfs:label ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -15228,348 +18835,546 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:object ], - [ sh:class biolink:SequenceVariant ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 34 ; + sh:path dct:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "A measurable quantity for the object of the association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 18 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:order 21 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 20 ; - sh:path biolink:category ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . - -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 31 ; + sh:path biolink:category ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:has_total ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:SequenceVariant ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:order 18 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:severity_qualifier ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:order 32 ; + sh:path rdf:type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "A measurable quantity for the object of the association" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . + +biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], [ sh:class biolink:InformationResource ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:class biolink:InformationResource ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 25 ; + sh:order 36 ; sh:path biolink:has_percentage ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 17 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:description "number of things with a particular property" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:has_count ], + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:InformationResource ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; + sh:order 38 ; sh:path biolink:onset_qualifier ], - [ sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:property [ sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_count ], + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 5 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:publications ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_total ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:order 22 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:InformationResource ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], [ sh:class biolink:InformationResource ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:knowledge_source ], - [ sh:description "number in object population that carry a particular allele, aka allele count" ; + [ sh:order 33 ; + sh:path rdf:type ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ], - [ sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_quotient ], + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; + sh:order 35 ; sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], + sh:order 2 ; + sh:path biolink:has_quotient ], [ sh:class biolink:InformationResource ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 21 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ] ; + sh:order 34 ; + sh:path rdfs:label ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Virus a sh:NodeShape ; sh:closed true ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15579,69 +19384,29 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:id ] ; sh:targetClass biolink:Virus . biolink:Agent a sh:NodeShape ; sh:closed true ; sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:address ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 9 ; sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:order 0 ; - sh:path biolink:affiliation ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15651,100 +19416,109 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:address ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:order 0 ; + sh:path biolink:affiliation ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Agent . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Occurrent ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_output ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], [ sh:class biolink:Occurrent ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path biolink:has_input ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 6 ; sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Occurrent ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_output ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -15754,6 +19528,20 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15763,21 +19551,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:BehavioralFeature . biolink:BiologicalProcess a sh:NodeShape ; @@ -15787,53 +19568,48 @@ biolink:BiologicalProcess a sh:NodeShape ; sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Occurrent ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path biolink:has_input ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Occurrent ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_output ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15842,40 +19618,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Occurrent ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path biolink:has_input ] ; sh:targetClass biolink:BiologicalProcess . biolink:Case a sh:NodeShape ; sh:closed true ; sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path dct:description ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15885,6 +19658,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], @@ -15898,7 +19679,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:CellLine a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -15907,25 +19692,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:order 6 ; sh:path rdf:type ], [ sh:class biolink:Attribute ; @@ -15933,22 +19704,39 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:CellLine . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -15957,36 +19745,29 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -15998,31 +19779,23 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 5 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16032,11 +19805,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -16047,63 +19815,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ] ; + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:ClinicalAttribute . biolink:Dataset a sh:NodeShape ; sh:closed true ; sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16112,32 +19878,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Dataset . biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:creation_date ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:property [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:license ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16151,65 +19919,67 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:rights ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:creation_date ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:distribution_download_url ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:license ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 3 ; sh:path biolink:format ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:rights ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; sh:closed true ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:order 5 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16218,44 +19988,25 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; sh:closed true ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -16268,58 +20019,75 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 15 ; sh:path dct:description ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Exon . - -biolink:GeneFamily a sh:NodeShape ; - sh:closed true ; - sh:description "any grouping of multiple genes or gene products related by common descent" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_metabolite ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; - sh:path dct:description ], + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; + sh:order 11 ; sh:path biolink:iri ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ] ; + sh:targetClass biolink:Exon . + +biolink:GeneFamily a sh:NodeShape ; + sh:closed true ; + sh:description "any grouping of multiple genes or gene products related by common descent" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -16328,24 +20096,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path dct:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:order 7 ; sh:path rdf:type ], [ sh:description "Alternate CURIEs for a thing" ; @@ -16354,7 +20130,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; @@ -16364,49 +20145,46 @@ biolink:GeneProductMixin a sh:NodeShape ; sh:property [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 2 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GeneProductMixin . biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 8 ; + sh:path dct:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16416,58 +20194,63 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:order 6 ; - sh:path rdf:type ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; sh:closed true ; sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 2 ; + sh:path biolink:format ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16476,40 +20259,43 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 9 ; - sh:path rdf:type ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:InformationContentEntity . biolink:OrganismalEntity a sh:NodeShape ; sh:closed true ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16519,16 +20305,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ] ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; sh:targetClass biolink:OrganismalEntity . biolink:Outcome a sh:NodeShape ; @@ -16542,41 +20323,53 @@ biolink:PredicateMapping a sh:NodeShape ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], + sh:order 5 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ], + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], [ sh:maxCount 1 ; sh:order 14 ; sh:path biolink:object_context_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:in [ rdf:rest () ] ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:narrow_match ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:object_part_qualifier ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_part_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:species_context_qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path rdf:predicate ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], - [ sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], [ sh:class biolink:NamedThing ; sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; sh:nodeKind sh:IRI ; @@ -16587,42 +20380,30 @@ biolink:PredicateMapping a sh:NodeShape ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:causal_mechanism_qualifier ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], [ sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:object_form_or_variant_qualifier ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ] ; + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:mapped_predicate ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; @@ -16634,6 +20415,18 @@ biolink:Procedure a sh:NodeShape ; sh:path biolink:provided_by ], [ sh:order 5 ; sh:path rdf:type ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16643,85 +20436,56 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 7 ; - sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ] ; + sh:path dct:description ] ; sh:targetClass biolink:Procedure . biolink:SocioeconomicAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16730,17 +20494,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Drug ; sh:description "connects an entity to one or more drugs" ; sh:nodeKind sh:IRI ; @@ -16751,26 +20551,6 @@ biolink:Treatment a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_device ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16780,13 +20560,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:timepoint ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], @@ -16800,26 +20581,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:Zygosity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16829,88 +20599,110 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Zygosity . biolink:Drug a sh:NodeShape ; sh:closed true ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path dct:description ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:is_supplement ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 11 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:trade_name ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16920,25 +20712,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 7 ; @@ -16949,22 +20730,31 @@ biolink:ExposureEvent a sh:NodeShape ; sh:closed true ; sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:ExposureEvent . biolink:IndividualOrganism a sh:NodeShape ; sh:closed true ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -16973,9 +20763,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 2 ; sh:path biolink:xref ], @@ -16984,58 +20776,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:order 6 ; sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:IndividualOrganism . biolink:MaterialSample a sh:NodeShape ; sh:closed true ; sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -17052,22 +20812,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:MaterialSample . biolink:Transcript a sh:NodeShape ; sh:closed true ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17078,45 +20864,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:is_metabolite ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:iri ], + [ sh:order 13 ; + sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; sh:path biolink:provided_by ], @@ -17124,28 +20902,41 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 14 ; sh:path rdfs:label ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 6 ; - sh:path biolink:max_tolerated_dose ] ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Transcript . biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:Occurrent ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17155,40 +20946,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Occurrent ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Occurrent ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path biolink:has_input ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; @@ -17197,7 +20969,16 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:enabled_by ] ; + sh:path biolink:enabled_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:Occurrent ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path biolink:has_input ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; @@ -17208,23 +20989,27 @@ biolink:LifeStage a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 2 ; sh:path biolink:xref ], @@ -17232,13 +21017,9 @@ biolink:LifeStage a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17254,57 +21035,38 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ], + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 14 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_metabolite ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:order 13 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 15 ; sh:path dct:description ], - [ sh:order 13 ; - sh:path rdf:type ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; @@ -17315,61 +21077,75 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ] ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 2 ; sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17378,7 +21154,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 5 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -17391,24 +21172,18 @@ biolink:MolecularActivity a sh:NodeShape ; sh:closed true ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -17419,101 +21194,111 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "The gene product, gene, or complex that catalyzes the reaction" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:order 9 ; - sh:path rdf:type ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:MolecularActivity . biolink:ChemicalMixture a sh:NodeShape ; sh:closed true ; sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalMixture ; + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "a human-readable description of an entity" ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:id ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:ChemicalEntity ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:order 14 ; sh:path rdf:type ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path dct:description ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; @@ -17528,14 +21313,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ChemicalMixture . biolink:MacromolecularMachineMixin a sh:NodeShape ; @@ -17552,45 +21333,20 @@ biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:description "" ; + sh:property [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:trade_name ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; @@ -17603,59 +21359,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "Alternate CURIEs for a thing" ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:order 11 ; - sh:path rdf:type ] ; - sh:targetClass biolink:MolecularEntity . - -biolink:PhenotypicFeature a sh:NodeShape ; - sh:closed true ; - sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 5 ; + sh:order 10 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_toxic ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; + sh:order 6 ; sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ] ; + sh:targetClass biolink:MolecularEntity . + +biolink:PhenotypicFeature a sh:NodeShape ; + sh:closed true ; + sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -17666,22 +21424,46 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:order 6 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PhenotypicFeature . biolink:PhysicalEntity a sh:NodeShape ; sh:closed true ; sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17691,63 +21473,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:order 5 ; - sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ] ; + sh:order 7 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PhysicalEntity . biolink:Genotype a sh:NodeShape ; sh:closed true ; sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path dct:description ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:order 8 ; + sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:class biolink:Zygosity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -17757,8 +21526,11 @@ biolink:Genotype a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:order 8 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17768,19 +21540,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 7 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ] ; + sh:order 9 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:class biolink:Zygosity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ] ; sh:targetClass biolink:Genotype . biolink:BiologicalSex a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17790,9 +21573,17 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 7 ; sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; @@ -17800,24 +21591,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:has_quantitative_value ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -17828,26 +21604,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:BiologicalSex . biolink:SequenceVariant a sh:NodeShape ; sh:closed true ; sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:order 8 ; sh:path rdf:type ], [ sh:class biolink:Gene ; @@ -17855,11 +21640,10 @@ biolink:SequenceVariant a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:order 1 ; @@ -17868,22 +21652,19 @@ biolink:SequenceVariant a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17899,60 +21680,34 @@ biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:property [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeature . - -biolink:Disease a sh:NodeShape ; - sh:closed true ; - sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17962,37 +21717,63 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeature . + +biolink:Disease a sh:NodeShape ; + sh:closed true ; + sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:Disease . biolink:Occurrent a sh:NodeShape ; @@ -18005,18 +21786,22 @@ biolink:Gene a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_biological_sequence ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 1 ; + sh:path biolink:synonym ], + [ sh:description "Symbol for a particular thing" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:symbol ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18026,22 +21811,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 1 ; - sh:path biolink:synonym ], - [ sh:description "Symbol for a particular thing" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:symbol ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:in_taxon ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; @@ -18050,29 +21824,33 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Gene . biolink:AnatomicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:order 6 ; - sh:path rdf:type ], + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18082,97 +21860,100 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 2 ; - sh:path biolink:xref ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:AnatomicalEntity . biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; sh:description " A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:ChemicalRole . biolink:GeneOrGeneProduct a sh:NodeShape ; @@ -18189,22 +21970,14 @@ biolink:Onset a sh:NodeShape ; sh:closed true ; sh:description "The age group in which (disease) symptom manifestations appear" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18214,57 +21987,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:Onset . biolink:SeverityValue a sh:NodeShape ; sh:closed true ; sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -18273,66 +22042,85 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 10 ; + sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:SeverityValue . biolink:QuantityValue a sh:NodeShape ; sh:closed true ; sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a quantity value to a unit" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_unit ], - [ sh:description "connects a quantity value to a number" ; + sh:property [ sh:description "connects a quantity value to a number" ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:has_numeric_value ] ; + sh:path biolink:has_numeric_value ], + [ sh:description "connects a quantity value to a unit" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_unit ] ; sh:targetClass biolink:QuantityValue . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "Alternate CURIEs for a thing" ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], @@ -18340,93 +22128,86 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:description "" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:is_toxic ], - [ sh:order 10 ; - sh:path rdf:type ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ChemicalEntity . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 7 ; sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18446,20 +22227,20 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:order 5 ; - sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path dct:description ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 1 ; sh:path biolink:xref ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -18468,6 +22249,10 @@ biolink:OrganismTaxon a sh:NodeShape ; [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18476,11 +22261,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:OrganismTaxon . biolink:EvidenceType a sh:NodeShape ; @@ -18488,40 +22269,44 @@ biolink:EvidenceType a sh:NodeShape ; sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18531,75 +22316,52 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ] ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:EvidenceType . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 16 ; sh:path dct:description ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:creation_date ], - [ sh:description "Alternate CURIEs for a thing" ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], [ sh:maxCount 1 ; sh:order 6 ; sh:path biolink:license ], + [ sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], + [ sh:description "Alternate CURIEs for a thing" ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18609,61 +22371,122 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ] ; sh:targetClass biolink:Publication . -biolink:OntologyClass a sh:NodeShape ; - sh:closed true ; - sh:description "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:OntologyClass . - -biolink:Attribute a sh:NodeShape ; +biolink:RetrievalSource a sh:NodeShape ; sh:closed true ; - sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; + sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 8 ; + sh:order 11 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:creation_date ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], + [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:resource_id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:rights ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + [ sh:description "Alternate CURIEs for a thing" ; sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:path biolink:xref ], + [ sh:order 12 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:license ], + [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:resource_role ] ; + sh:targetClass biolink:RetrievalSource . + +biolink:Attribute a sh:NodeShape ; + sh:closed true ; + sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; @@ -18675,48 +22498,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ] ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Attribute . biolink:InformationResource a sh:NodeShape ; sh:closed true ; sh:description "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:description "Alternate CURIEs for a thing" ; sh:order 5 ; sh:path biolink:xref ], @@ -18724,18 +22547,17 @@ biolink:InformationResource a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18744,7 +22566,39 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:InformationResource . +biolink:OntologyClass a sh:NodeShape ; + sh:closed true ; + sh:description "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:OntologyClass . + diff --git a/biolink-model.shexj b/biolink-model.shexj index b1a25ea244..03ba8fcb38 100644 --- a/biolink-model.shexj +++ b/biolink-model.shexj @@ -908,6 +908,83 @@ "min": 0, "max": 1 }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_category", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_category", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_category_closure", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_category_closure", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_namespace", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_namespace", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_label_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_label_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/retrieval_source_ids", + "valueExpr": "https://w3id.org/biolink/vocab/RetrievalSource", + "min": 0, + "max": -1 + }, { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", @@ -14560,7 +14637,7 @@ }, { "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/resource", + "predicate": "https://w3id.org/biolink/vocab/resource_id", "valueExpr": "https://w3id.org/linkml/Uriorcurie", "min": 1, "max": 1 @@ -14574,7 +14651,7 @@ }, { "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/upstream_resources", + "predicate": "https://w3id.org/biolink/vocab/upstream_resource_ids", "valueExpr": "https://w3id.org/linkml/Uriorcurie", "min": 0, "max": 1 diff --git a/biolink-model.ttl b/biolink-model.ttl index 137b1a4087..ce91e46099 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -331,270 +331,270 @@ , , ; - linkml:generation_date "2023-03-30T15:49:08"^^xsd:dateTime ; + linkml:generation_date "2023-04-03T20:56:29"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "metacyc.reaction" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DOID-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.food" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "gff3" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "OMIM.PS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VMC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCIT-OBO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ncats.drug" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-TOPIC" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HsapDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "bioschemas" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "AspGD" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MmusDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "medgen" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CTD.GENE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEED.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "orphanet" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PHARMGKB.PATHWAYS" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "CTD.CHEMICAL" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEED.REACTION" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.ENZYME" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.CHEMICAL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ncats.drug" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcid" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OMIM.PS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "mirbase" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mmmp.biomaps" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UMLSSG" ; linkml:prefix_reference ], [ linkml:prefix_prefix "ComplexPortal" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "RXCUI" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "HANCESTRO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.VARIANT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.ENZYME" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UBERGRAPH" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ncats.bioplanet" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NBO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PHARMGKB.DISEASE" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "WBls" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "RO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.food" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference OIO: ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "AGRKB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_CORE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UniProtKB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCIT-OBO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "VANDF" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "STY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UNIPROT.ISOFORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VMC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PomBase" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYECO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.VARIANT" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBbt" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.DISEASE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "orphanet" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "FYPO" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.DISEASE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MmusDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBbt" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ScopusID" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CAID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "mmmp.biomaps" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UniProtKB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcid" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "metacyc.reaction" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SPDI" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference OIO: ], + [ linkml:prefix_prefix "EDAM-TOPIC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.PATHWAY" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "wgs" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.DGROUP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBls" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYECO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema: ], [ linkml:prefix_prefix "foodb.compound" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "UO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.CHEMICAL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DOID-PROPERTY" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_CORE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "DrugCentral" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "NBO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UNIPROT.ISOFORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "METANETX.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ncats.bioplanet" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "AGRKB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.DGROUP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], + [ linkml:prefix_prefix "SPDI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -1063,11 +1063,16 @@ , , , + , + , + , , , , , + , , + , , , , @@ -1161,14 +1166,15 @@ , , , - , + , , , , , - , + , + , , - , + , , , , @@ -1204,11 +1210,16 @@ , , , + , + , + , , , , , + , , + , , , , @@ -1249,7 +1260,7 @@ , , , - , + , , , , @@ -1271,8 +1282,8 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2023-03-30T15:47:28"^^xsd:dateTime ; - linkml:source_file_size 341681 ; + linkml:source_file_date "2023-04-03T20:54:34"^^xsd:dateTime ; + linkml:source_file_size 348255 ; linkml:subsets , , , @@ -2256,9 +2267,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "human" ], + skos:example "zebrafish" ], [ a linkml:Example ; - skos:example "zebrafish" ] ; + skos:example "human" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -2544,9 +2555,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "blood" ], + skos:example "cerebral cortext" ], [ a linkml:Example ; - skos:example "cerebral cortext" ] ; + skos:example "blood" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -3509,14 +3520,14 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; + skos:definition "abnormal circulating bilirubin level" ; + skos:example "MP:0001569" ], + [ a linkml:Example ; skos:definition "Hyperkinesis" ; skos:example "HP:0002487" ], [ a linkml:Example ; skos:definition "axon morphology variant" ; - skos:example "WBPhenotype:0000180" ], - [ a linkml:Example ; - skos:definition "abnormal circulating bilirubin level" ; - skos:example "MP:0001569" ] ; + skos:example "WBPhenotype:0000180" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -5727,21 +5738,21 @@ linkml:slot_uri rdf:object ; linkml:usage_slot_name "object" . - a linkml:SlotDefinition ; + a linkml:SlotDefinition ; OIO:inSubset ; skos:definition "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; skos:inScheme ; - linkml:alias "resource" ; - linkml:definition_uri ; + linkml:alias "resource id" ; + linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; linkml:range ; linkml:required true ; - linkml:slot_uri ; - linkml:usage_slot_name "resource" . + linkml:slot_uri ; + linkml:usage_slot_name "resource id" . a linkml:SlotDefinition ; OIO:inSubset ; @@ -5759,19 +5770,19 @@ linkml:slot_uri ; linkml:usage_slot_name "resource role" . - a linkml:SlotDefinition ; + a linkml:SlotDefinition ; skos:definition "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; skos:inScheme ; - linkml:alias "upstream resources" ; - linkml:definition_uri ; + linkml:alias "upstream resource ids" ; + linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; linkml:range ; - linkml:slot_uri ; - linkml:usage_slot_name "upstream resources" . + linkml:slot_uri ; + linkml:usage_slot_name "upstream resource ids" . a linkml:SlotDefinition ; skos:definition "treatment whose efficacy is modulated by the subject variant" ; @@ -6120,11 +6131,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "chr13:g.32921033G>C (hg19) in ClinGen" ; - skos:example "ClinGen:CA024716" ], - [ a linkml:Example ; skos:definition "CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)" ; - skos:example "CLINVAR:38077" ] ; + skos:example "CLINVAR:38077" ], + [ a linkml:Example ; + skos:definition "chr13:g.32921033G>C (hg19) in ClinGen" ; + skos:example "ClinGen:CA024716" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; @@ -6398,6 +6409,11 @@ , , , + , + , + , + , + , , , , @@ -6406,9 +6422,15 @@ , , , + , , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -6687,6 +6709,11 @@ , , , + , + , + , + , + , , , , @@ -6694,7 +6721,13 @@ , , , + , , + , + , + , + , + , . skos:definition "" ; @@ -7157,6 +7190,11 @@ , , , + , + , + , + , + , , , , @@ -7164,7 +7202,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -8729,6 +8773,11 @@ , , , + , + , + , + , + , , , , @@ -8736,7 +8785,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -9055,6 +9110,11 @@ , , , + , + , + , + , + , , , , @@ -9062,7 +9122,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -9937,11 +10003,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "positively correlated with" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "positively correlated with" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10568,6 +10634,11 @@ , , , + , + , + , + , + , , , , @@ -10575,7 +10646,13 @@ , , , + , , + , + , + , + , + , . a linkml:SlotDefinition ; @@ -11251,11 +11328,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "treats" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "treats" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11475,11 +11552,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "prevents" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "prevents" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11650,11 +11727,11 @@ skos:inScheme ; skos:mappingRelation ; linkml:annotations [ a linkml:Annotation ; - skos:example "is excipient of" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "is excipient of" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11806,11 +11883,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has decreased amount" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12183,11 +12260,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "decreases response to" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "decreases response to" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12466,11 +12543,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has part" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -13384,6 +13461,11 @@ , , , + , + , + , + , + , , , , @@ -13392,7 +13474,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13477,13 +13565,24 @@ , , , + , + , + , + , + , , , , , , , + , , + , + , + , + , + , . skos:inScheme ; @@ -13520,6 +13619,11 @@ , , , + , + , + , + , + , , , , @@ -13527,7 +13631,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13592,6 +13702,11 @@ , , , + , + , + , + , + , , , , @@ -13599,7 +13714,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13625,6 +13746,11 @@ , , , + , + , + , + , + , , , , @@ -13632,7 +13758,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13672,6 +13804,11 @@ , , , + , + , + , + , + , , , , @@ -13680,8 +13817,14 @@ , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13709,6 +13852,11 @@ , , , + , + , + , + , + , , , , @@ -13717,7 +13865,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13747,6 +13901,11 @@ , , , + , + , + , + , + , , , , @@ -13754,7 +13913,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13809,6 +13974,11 @@ , , , + , + , + , + , + , , , , @@ -13816,7 +13986,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13865,6 +14041,11 @@ , , , + , + , + , + , + , , , , @@ -13872,6 +14053,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13895,6 +14082,11 @@ , , , + , + , + , + , + , , , , @@ -13902,6 +14094,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13925,6 +14123,11 @@ , , , + , + , + , + , + , , , , @@ -13932,6 +14135,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -13958,6 +14167,11 @@ , , , + , + , + , + , + , , , , @@ -13967,7 +14181,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -14103,6 +14323,11 @@ , , , + , + , + , + , + , , , , @@ -14114,7 +14339,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -14233,6 +14464,11 @@ , , , + , + , + , + , + , , , , @@ -14240,7 +14476,13 @@ , , , + , , + , + , + , + , + , , , , @@ -14270,6 +14512,11 @@ , , , + , + , + , + , + , , , , @@ -14277,8 +14524,14 @@ , , , + , , , + , + , + , + , + , , , . @@ -14310,6 +14563,11 @@ , , , + , + , + , + , + , , , , @@ -14318,8 +14576,14 @@ , , , + , , , + , + , + , + , + , , . @@ -14393,10 +14657,10 @@ linkml:domain ; linkml:examples [ a linkml:Example ; skos:example "stability" ], - [ a linkml:Example ; - skos:example "expression" ], [ a linkml:Example ; skos:example "abundance" ], + [ a linkml:Example ; + skos:example "expression" ], [ a linkml:Example ; skos:example "exposure" ] ; linkml:is_a ; @@ -14525,9 +14789,9 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "cohort x (e.g. a specific population, referenced by an identifier)" ], + skos:example "gut microbiome" ], [ a linkml:Example ; - skos:example "gut microbiome" ] ; + skos:example "cohort x (e.g. a specific population, referenced by an identifier)" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -14654,13 +14918,13 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "transplant" ], + skos:example "mutation" ], [ a linkml:Example ; skos:example "chemical analog" ], [ a linkml:Example ; skos:example "late stage" ], [ a linkml:Example ; - skos:example "mutation" ], + skos:example "transplant" ], [ a linkml:Example ; skos:example "severe" ] ; linkml:is_a ; @@ -14679,11 +14943,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "postsynaptic membrane" ; - skos:example "GO:0045211" ], - [ a linkml:Example ; skos:definition "kinase activity" ; - skos:example "GO:0016301" ] ; + skos:example "GO:0016301" ], + [ a linkml:Example ; + skos:definition "postsynaptic membrane" ; + skos:example "GO:0045211" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -15362,17 +15626,17 @@ linkml:slot_uri ; linkml:symmetric true . - a linkml:SlotDefinition ; + a linkml:SlotDefinition ; OIO:inSubset ; skos:definition "The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; skos:inScheme ; - linkml:definition_uri ; + linkml:definition_uri ; linkml:domain ; linkml:domain_of ; linkml:is_a ; linkml:owner ; linkml:range ; - linkml:slot_uri . + linkml:slot_uri . a linkml:SlotDefinition ; OIO:inSubset ; @@ -15453,16 +15717,16 @@ linkml:slot_uri ; linkml:symmetric true . - a linkml:SlotDefinition ; + a linkml:SlotDefinition ; skos:definition "An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact." ; skos:inScheme ; - linkml:definition_uri ; + linkml:definition_uri ; linkml:domain ; linkml:domain_of ; linkml:is_a ; linkml:owner ; linkml:range ; - linkml:slot_uri . + linkml:slot_uri . a linkml:ClassDefinition ; skos:definition "An abstract association for use where the case is the subject" ; @@ -15496,6 +15760,11 @@ , , , + , + , + , + , + , , , , @@ -15503,6 +15772,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -15619,6 +15894,11 @@ , , , + , + , + , + , + , , , , @@ -15627,7 +15907,13 @@ , , , + , , + , + , + , + , + , , . @@ -15686,6 +15972,11 @@ , , , + , + , + , + , + , , , , @@ -15693,6 +15984,12 @@ , , , + , + , + , + , + , + , . skos:closeMatch , @@ -16063,6 +16360,11 @@ , , , + , + , + , + , + , , , , @@ -16070,7 +16372,13 @@ , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16579,6 +16887,11 @@ , , , + , + , + , + , + , , , , @@ -16587,8 +16900,14 @@ , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16647,13 +16966,24 @@ , , , + , + , + , + , + , , , , , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16680,6 +17010,11 @@ , , , + , + , + , + , + , , , , @@ -16687,6 +17022,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16710,13 +17051,24 @@ , , , + , + , + , + , + , , , , , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16749,6 +17101,11 @@ , , , + , + , + , + , + , , , , @@ -16757,8 +17114,14 @@ , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16795,6 +17158,11 @@ , , , + , + , + , + , + , , , , @@ -16802,6 +17170,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16827,6 +17201,11 @@ , , , + , + , + , + , + , , , , @@ -16834,6 +17213,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16859,6 +17244,11 @@ , , , + , + , + , + , + , , , , @@ -16866,6 +17256,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16897,6 +17293,11 @@ , , , + , + , + , + , + , , , , @@ -16905,8 +17306,14 @@ , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16939,6 +17346,11 @@ , , , + , + , + , + , + , , , , @@ -16946,8 +17358,14 @@ , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -16979,6 +17397,11 @@ , , , + , + , + , + , + , , , , @@ -16986,6 +17409,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -17008,6 +17437,11 @@ , , , + , + , + , + , + , , , , @@ -17015,6 +17449,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -17037,6 +17477,11 @@ , , , + , + , + , + , + , , , , @@ -17046,6 +17491,12 @@ , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -17078,6 +17529,11 @@ , , , + , + , + , + , + , , , , @@ -17085,8 +17541,14 @@ , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -17109,6 +17571,11 @@ , , , + , + , + , + , + , , , , @@ -17116,6 +17583,12 @@ , , , + , + , + , + , + , + , , , . @@ -17140,6 +17613,11 @@ , , , + , + , + , + , + , , , , @@ -17147,6 +17625,12 @@ , , , + , + , + , + , + , + , , , . @@ -17422,13 +17906,24 @@ , , , + , + , + , + , + , , , , , , , + , , + , + , + , + , + , , , . @@ -17566,11 +18061,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "lacks part" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "lacks part" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -17817,6 +18312,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -17824,6 +18324,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -17955,6 +18461,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -17964,6 +18475,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18187,12 +18704,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18217,12 +18745,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18245,12 +18784,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18290,6 +18840,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -18297,7 +18852,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18345,6 +18906,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -18353,7 +18919,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18380,6 +18952,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -18387,6 +18964,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18413,12 +18996,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18445,12 +19039,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18476,12 +19081,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18507,12 +19123,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18538,12 +19165,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18569,12 +19207,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18601,12 +19250,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18632,12 +19292,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18661,12 +19332,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18688,6 +19370,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -18697,6 +19384,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18718,6 +19411,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -18727,6 +19425,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18757,6 +19461,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -18766,6 +19475,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -18789,6 +19504,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -18796,8 +19516,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19146,6 +19872,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -19153,6 +19884,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19181,6 +19918,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -19188,7 +19930,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19212,6 +19960,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -19222,7 +19975,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19248,6 +20007,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -19255,7 +20019,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , + , + , + , + , + , , , , @@ -19298,11 +20068,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "has input" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has input" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -19368,6 +20138,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -19375,8 +20150,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , + , + , + , , + , + , . a linkml:ClassDefinition ; @@ -19550,11 +20331,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19811,12 +20603,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19851,12 +20654,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19929,6 +20743,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -19939,6 +20758,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -19962,6 +20787,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -19972,6 +20802,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -20015,13 +20851,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -20049,6 +20896,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -20056,6 +20908,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , + , , , , @@ -20247,12 +21105,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -20300,31 +21169,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , - . - - a linkml:ClassDefinition ; - skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , + , , . @@ -20385,6 +21230,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:ClassDefinition ; + skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; + skos:inScheme ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:SlotDefinition ; skos:definition "" ; skos:inScheme ; @@ -20760,6 +21629,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , @@ -20767,8 +21641,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , , + , + , + , + , + , . a linkml:ClassDefinition ; @@ -21020,11 +21900,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; skos:note "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" ; linkml:alt_descriptions [ a linkml:AltDescription ; - skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; - linkml:source "AGR" ], - [ a linkml:AltDescription ; skos:definition "A contiguous change at a Location" ; - linkml:source "VMC" ] ; + linkml:source "VMC" ], + [ a linkml:AltDescription ; + skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; + linkml:source "AGR" ] ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "AGRKB", @@ -21101,34 +21981,25 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . - a linkml:ClassDefinition ; - rdfs:seeAlso ; - skos:definition "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - skos:exactMatch schema:Class, - owl:Class ; - skos:inScheme ; - skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", - "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:examples [ a linkml:Example ; - skos:definition "the class 'brain' from the Uberon anatomy ontology" ; - skos:example "UBERON:0000955" ] ; - linkml:id_prefixes "KEGG.BRITE", - "MESH", - "UMLS" ; - linkml:mixin true ; - linkml:slot_usage [ ] ; - linkml:slots . - a linkml:ClassDefinition ; skos:definition "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; skos:inScheme ; @@ -21173,20 +22044,25 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . - a linkml:SlotDefinition ; - skos:altLabel "edge property", - "edge qualifier", - "node qualifier", - "statement property", - "statement qualifier" ; - skos:definition "any slot that relates an association to another entity" ; + a linkml:ClassDefinition ; + rdfs:seeAlso ; + skos:definition "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; + skos:exactMatch schema:Class, + owl:Class ; skos:inScheme ; - linkml:abstract true ; - linkml:definition_uri ; - linkml:domain ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . + skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", + "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:examples [ a linkml:Example ; + skos:definition "the class 'brain' from the Uberon anatomy ontology" ; + skos:example "UBERON:0000955" ] ; + linkml:id_prefixes "KEGG.BRITE", + "MESH", + "UMLS" ; + linkml:mixin true ; + linkml:slot_usage [ ] ; + linkml:slots . a linkml:SlotDefinition ; OIO:inSubset ; @@ -21223,6 +22099,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + skos:altLabel "edge property", + "edge qualifier", + "node qualifier", + "statement property", + "statement qualifier" ; + skos:definition "any slot that relates an association to another entity" ; + skos:inScheme ; + linkml:abstract true ; + linkml:definition_uri ; + linkml:domain ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:ClassDefinition ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; skos:inScheme ; @@ -21259,12 +22150,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , + , + , , , , , , , + , + , + , + , + , + , . a linkml:SlotDefinition ; @@ -21335,6 +22237,80 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + skos:definition "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The object category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Disease'." ; + skos:example "biolink:Disease" ] ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The object category closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all biolink classes that are ancestors of 'biolink:Disease' in the biolink model. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well." ; + skos:example "['biolink:Disease', 'biolink:NamedThing']" ] ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The object closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all diseases that are ancestors of 'breast cancer' in the MONDO ontology. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well." ; + skos:example "['MONDO:0000167', 'MONDO:0005395']" ] ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The object label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'breast cancer' in the biolink model." ; + skos:example "['breast cancer', 'cancer']" ] ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:altLabel "object prefix" ; + skos:definition "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The object namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'MONDO'." ; + skos:example "MONDO" ] ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; skos:definition "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; skos:inScheme ; @@ -21387,6 +22363,88 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain_of ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The subject category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Gene'." ; + skos:example "biolink:Gene" ] ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The subject category closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all biolink classes that are ancestors of 'biolink:Gene' in the biolink model. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well." ; + skos:example "['biolink:Gene', 'biolink:NamedThing']" ] ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The subject label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'BRCA1' in the biolink model. " ; + skos:example "['BRACA1']" ] ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:altLabel "subject prefix" ; + skos:definition "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "The subject namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'NCBIGene'." ; + skos:example "NCBIGene" ] ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; skos:definition "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; skos:editorialNote "For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP- generated knowledge is \"infores:unc-cdw-health.\" The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"" ; @@ -21546,11 +22604,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "predicate" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "annotation predicate" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -21570,39 +22628,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri rdf:type . - a linkml:ClassDefinition ; - skos:definition "A typed association between two entities, supported by evidence" ; - skos:exactMatch rdf:Statement, - owl:Axiom, - ; - skos:inScheme ; - skos:note "This is roughly the model used by biolink and ontobio at the moment" ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - a linkml:SlotDefinition ; skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; skos:exactMatch , @@ -21672,6 +22697,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:required true ; linkml:slot_uri rdf:subject . + a linkml:ClassDefinition ; + skos:definition "A typed association between two entities, supported by evidence" ; + skos:exactMatch rdf:Statement, + owl:Axiom, + ; + skos:inScheme ; + skos:note "This is roughly the model used by biolink and ontobio at the moment" ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:SlotDefinition ; OIO:inSubset ; skos:closeMatch ; diff --git a/biolink-modeln.shex b/biolink-modeln.shex index 89b98ac9b3..69e80dc0bd 100644 --- a/biolink-modeln.shex +++ b/biolink-modeln.shex @@ -208,6 +208,17 @@ linkml:Nodeidentifier NONLITERAL @linkml:String ? ; @linkml:Uriorcurie ? ; @linkml:String ? ; + @ ? ; + @ ? ; + @linkml:String * ; + @linkml:String * ; + @ * ; + @ * ; + @linkml:String ? ; + @linkml:String ? ; + @linkml:String * ; + @linkml:String * ; + @ * ; @linkml:String * ; @ * ) ; @@ -2847,9 +2858,9 @@ linkml:Nodeidentifier NONLITERAL CLOSED { ( $ ( & ; rdf:type [ ] ? ; - @linkml:Uriorcurie ; + @linkml:Uriorcurie ; @ ; - @linkml:Uriorcurie ? + @linkml:Uriorcurie ? ) ; rdf:type [ ] ) diff --git a/biolink-modeln.shexj b/biolink-modeln.shexj index 716c25dc51..66e54e2acd 100644 --- a/biolink-modeln.shexj +++ b/biolink-modeln.shexj @@ -908,6 +908,83 @@ "min": 0, "max": 1 }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_category", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_category", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_category_closure", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_category_closure", + "valueExpr": "https://w3id.org/biolink/vocab/OntologyClass", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_namespace", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_namespace", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_label_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_label_closure", + "valueExpr": "https://w3id.org/linkml/String", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/retrieval_source_ids", + "valueExpr": "https://w3id.org/biolink/vocab/RetrievalSource", + "min": 0, + "max": -1 + }, { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/type", @@ -14560,7 +14637,7 @@ }, { "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/resource", + "predicate": "https://w3id.org/biolink/vocab/resource_id", "valueExpr": "https://w3id.org/linkml/Uriorcurie", "min": 1, "max": 1 @@ -14574,7 +14651,7 @@ }, { "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/upstream_resources", + "predicate": "https://w3id.org/biolink/vocab/upstream_resource_ids", "valueExpr": "https://w3id.org/linkml/Uriorcurie", "min": 0, "max": 1 diff --git a/biolink/model.py b/biolink/model.py index 45f771a3d0..e9ca6f9d36 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-03-30T15:49:20 +# Generation date: 2023-04-03T20:56:43 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -2635,9 +2635,9 @@ class RetrievalSource(InformationContentEntity): id: Union[str, RetrievalSourceId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - resource: Union[str, URIorCURIE] = None + resource_id: Union[str, URIorCURIE] = None resource_role: Union[str, "ResourceRoleEnum"] = None - upstream_resources: Optional[Union[str, URIorCURIE]] = None + upstream_resource_ids: Optional[Union[str, URIorCURIE]] = None xref: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -2646,18 +2646,18 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.id, RetrievalSourceId): self.id = RetrievalSourceId(self.id) - if self._is_empty(self.resource): - self.MissingRequiredField("resource") - if not isinstance(self.resource, URIorCURIE): - self.resource = URIorCURIE(self.resource) + if self._is_empty(self.resource_id): + self.MissingRequiredField("resource_id") + if not isinstance(self.resource_id, URIorCURIE): + self.resource_id = URIorCURIE(self.resource_id) if self._is_empty(self.resource_role): self.MissingRequiredField("resource_role") if not isinstance(self.resource_role, ResourceRoleEnum): self.resource_role = ResourceRoleEnum(self.resource_role) - if self.upstream_resources is not None and not isinstance(self.upstream_resources, URIorCURIE): - self.upstream_resources = URIorCURIE(self.upstream_resources) + if self.upstream_resource_ids is not None and not isinstance(self.upstream_resource_ids, URIorCURIE): + self.upstream_resource_ids = URIorCURIE(self.upstream_resource_ids) if not isinstance(self.xref, list): self.xref = [self.xref] if self.xref is not None else [] @@ -5993,6 +5993,17 @@ class Association(Entity): original_subject: Optional[str] = None original_predicate: Optional[Union[str, URIorCURIE]] = None original_object: Optional[str] = None + subject_category: Optional[Union[str, OntologyClassId]] = None + object_category: Optional[Union[str, OntologyClassId]] = None + subject_closure: Optional[Union[str, List[str]]] = empty_list() + object_closure: Optional[Union[str, List[str]]] = empty_list() + subject_category_closure: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() + object_category_closure: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() + subject_namespace: Optional[str] = None + object_namespace: Optional[str] = None + subject_label_closure: Optional[Union[str, List[str]]] = empty_list() + object_label_closure: Optional[Union[str, List[str]]] = empty_list() + retrieval_source_ids: Optional[Union[Union[str, RetrievalSourceId], List[Union[str, RetrievalSourceId]]]] = empty_list() type: Optional[Union[str, List[str]]] = empty_list() category: Optional[Union[Union[str, CategoryType], List[Union[str, CategoryType]]]] = empty_list() @@ -6054,6 +6065,46 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.original_object is not None and not isinstance(self.original_object, str): self.original_object = str(self.original_object) + if self.subject_category is not None and not isinstance(self.subject_category, OntologyClassId): + self.subject_category = OntologyClassId(self.subject_category) + + if self.object_category is not None and not isinstance(self.object_category, OntologyClassId): + self.object_category = OntologyClassId(self.object_category) + + if not isinstance(self.subject_closure, list): + self.subject_closure = [self.subject_closure] if self.subject_closure is not None else [] + self.subject_closure = [v if isinstance(v, str) else str(v) for v in self.subject_closure] + + if not isinstance(self.object_closure, list): + self.object_closure = [self.object_closure] if self.object_closure is not None else [] + self.object_closure = [v if isinstance(v, str) else str(v) for v in self.object_closure] + + if not isinstance(self.subject_category_closure, list): + self.subject_category_closure = [self.subject_category_closure] if self.subject_category_closure is not None else [] + self.subject_category_closure = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.subject_category_closure] + + if not isinstance(self.object_category_closure, list): + self.object_category_closure = [self.object_category_closure] if self.object_category_closure is not None else [] + self.object_category_closure = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.object_category_closure] + + if self.subject_namespace is not None and not isinstance(self.subject_namespace, str): + self.subject_namespace = str(self.subject_namespace) + + if self.object_namespace is not None and not isinstance(self.object_namespace, str): + self.object_namespace = str(self.object_namespace) + + if not isinstance(self.subject_label_closure, list): + self.subject_label_closure = [self.subject_label_closure] if self.subject_label_closure is not None else [] + self.subject_label_closure = [v if isinstance(v, str) else str(v) for v in self.subject_label_closure] + + if not isinstance(self.object_label_closure, list): + self.object_label_closure = [self.object_label_closure] if self.object_label_closure is not None else [] + self.object_label_closure = [v if isinstance(v, str) else str(v) for v in self.object_label_closure] + + if not isinstance(self.retrieval_source_ids, list): + self.retrieval_source_ids = [self.retrieval_source_ids] if self.retrieval_source_ids is not None else [] + self.retrieval_source_ids = [v if isinstance(v, RetrievalSourceId) else RetrievalSourceId(v) for v in self.retrieval_source_ids] + if not isinstance(self.type, list): self.type = [self.type] if self.type is not None else [] self.type = [v if isinstance(v, str) else str(v) for v in self.type] @@ -10132,17 +10183,20 @@ class slots: slots.support_graphs = Slot(uri=BIOLINK.support_graphs, name="support graphs", curie=BIOLINK.curie('support_graphs'), model_uri=BIOLINK.support_graphs, domain=None, range=Optional[Union[str, List[str]]]) -slots.resource = Slot(uri=BIOLINK.resource, name="resource", curie=BIOLINK.curie('resource'), - model_uri=BIOLINK.resource, domain=RetrievalSource, range=Optional[Union[str, URIorCURIE]]) +slots.resource_id = Slot(uri=BIOLINK.resource_id, name="resource id", curie=BIOLINK.curie('resource_id'), + model_uri=BIOLINK.resource_id, domain=RetrievalSource, range=Optional[Union[str, URIorCURIE]]) slots.resource_role = Slot(uri=BIOLINK.resource_role, name="resource role", curie=BIOLINK.curie('resource_role'), model_uri=BIOLINK.resource_role, domain=RetrievalSource, range=Optional[Union[str, "ResourceRoleEnum"]]) +slots.retrieval_source_ids = Slot(uri=BIOLINK.retrieval_source_ids, name="retrieval source ids", curie=BIOLINK.curie('retrieval_source_ids'), + model_uri=BIOLINK.retrieval_source_ids, domain=None, range=Optional[Union[Union[str, RetrievalSourceId], List[Union[str, RetrievalSourceId]]]]) + slots.full_name = Slot(uri=BIOLINK.full_name, name="full name", curie=BIOLINK.curie('full_name'), model_uri=BIOLINK.full_name, domain=NamedThing, range=Optional[Union[str, LabelType]]) -slots.upstream_resources = Slot(uri=BIOLINK.upstream_resources, name="upstream resources", curie=BIOLINK.curie('upstream_resources'), - model_uri=BIOLINK.upstream_resources, domain=RetrievalSource, range=Optional[Union[str, URIorCURIE]]) +slots.upstream_resource_ids = Slot(uri=BIOLINK.upstream_resource_ids, name="upstream resource ids", curie=BIOLINK.curie('upstream_resource_ids'), + model_uri=BIOLINK.upstream_resource_ids, domain=RetrievalSource, range=Optional[Union[str, URIorCURIE]]) slots.description = Slot(uri=DCT.description, name="description", curie=DCT.curie('description'), model_uri=BIOLINK.description, domain=None, range=Optional[Union[str, NarrativeText]]) @@ -11161,6 +11215,36 @@ class slots: slots.original_predicate = Slot(uri=BIOLINK.original_predicate, name="original predicate", curie=BIOLINK.curie('original_predicate'), model_uri=BIOLINK.original_predicate, domain=Association, range=Optional[Union[str, URIorCURIE]]) +slots.subject_closure = Slot(uri=BIOLINK.subject_closure, name="subject closure", curie=BIOLINK.curie('subject_closure'), + model_uri=BIOLINK.subject_closure, domain=Association, range=Optional[Union[str, List[str]]]) + +slots.object_closure = Slot(uri=BIOLINK.object_closure, name="object closure", curie=BIOLINK.curie('object_closure'), + model_uri=BIOLINK.object_closure, domain=Association, range=Optional[Union[str, List[str]]]) + +slots.subject_category = Slot(uri=BIOLINK.subject_category, name="subject category", curie=BIOLINK.curie('subject_category'), + model_uri=BIOLINK.subject_category, domain=Association, range=Optional[Union[str, OntologyClassId]]) + +slots.object_category = Slot(uri=BIOLINK.object_category, name="object category", curie=BIOLINK.curie('object_category'), + model_uri=BIOLINK.object_category, domain=Association, range=Optional[Union[str, OntologyClassId]]) + +slots.subject_category_closure = Slot(uri=BIOLINK.subject_category_closure, name="subject category closure", curie=BIOLINK.curie('subject_category_closure'), + model_uri=BIOLINK.subject_category_closure, domain=Association, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) + +slots.object_category_closure = Slot(uri=BIOLINK.object_category_closure, name="object category closure", curie=BIOLINK.curie('object_category_closure'), + model_uri=BIOLINK.object_category_closure, domain=Association, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) + +slots.subject_label_closure = Slot(uri=BIOLINK.subject_label_closure, name="subject label closure", curie=BIOLINK.curie('subject_label_closure'), + model_uri=BIOLINK.subject_label_closure, domain=Association, range=Optional[Union[str, List[str]]]) + +slots.object_label_closure = Slot(uri=BIOLINK.object_label_closure, name="object label closure", curie=BIOLINK.curie('object_label_closure'), + model_uri=BIOLINK.object_label_closure, domain=Association, range=Optional[Union[str, List[str]]]) + +slots.subject_namespace = Slot(uri=BIOLINK.subject_namespace, name="subject namespace", curie=BIOLINK.curie('subject_namespace'), + model_uri=BIOLINK.subject_namespace, domain=Association, range=Optional[str]) + +slots.object_namespace = Slot(uri=BIOLINK.object_namespace, name="object namespace", curie=BIOLINK.curie('object_namespace'), + model_uri=BIOLINK.object_namespace, domain=Association, range=Optional[str]) + slots.subject = Slot(uri=RDF.subject, name="subject", curie=RDF.curie('subject'), model_uri=BIOLINK.subject, domain=Association, range=Union[str, NamedThingId]) @@ -11393,14 +11477,14 @@ class slots: slots.article_iso_abbreviation = Slot(uri=BIOLINK.iso_abbreviation, name="article_iso abbreviation", curie=BIOLINK.curie('iso_abbreviation'), model_uri=BIOLINK.article_iso_abbreviation, domain=Article, range=Optional[str]) -slots.retrieval_source_resource = Slot(uri=BIOLINK.resource, name="retrieval source_resource", curie=BIOLINK.curie('resource'), - model_uri=BIOLINK.retrieval_source_resource, domain=RetrievalSource, range=Union[str, URIorCURIE]) +slots.retrieval_source_resource_id = Slot(uri=BIOLINK.resource_id, name="retrieval source_resource id", curie=BIOLINK.curie('resource_id'), + model_uri=BIOLINK.retrieval_source_resource_id, domain=RetrievalSource, range=Union[str, URIorCURIE]) slots.retrieval_source_resource_role = Slot(uri=BIOLINK.resource_role, name="retrieval source_resource role", curie=BIOLINK.curie('resource_role'), model_uri=BIOLINK.retrieval_source_resource_role, domain=RetrievalSource, range=Union[str, "ResourceRoleEnum"]) -slots.retrieval_source_upstream_resources = Slot(uri=BIOLINK.upstream_resources, name="retrieval source_upstream resources", curie=BIOLINK.curie('upstream_resources'), - model_uri=BIOLINK.retrieval_source_upstream_resources, domain=RetrievalSource, range=Optional[Union[str, URIorCURIE]]) +slots.retrieval_source_upstream_resource_ids = Slot(uri=BIOLINK.upstream_resource_ids, name="retrieval source_upstream resource ids", curie=BIOLINK.curie('upstream_resource_ids'), + model_uri=BIOLINK.retrieval_source_upstream_resource_ids, domain=RetrievalSource, range=Optional[Union[str, URIorCURIE]]) slots.small_molecule_id = Slot(uri=BIOLINK.id, name="small molecule_id", curie=BIOLINK.curie('id'), model_uri=BIOLINK.small_molecule_id, domain=SmallMolecule, range=Union[str, SmallMoleculeId]) diff --git a/biolink/pydanticmodel.py b/biolink/pydanticmodel.py index 807c3442e2..52523bce75 100644 --- a/biolink/pydanticmodel.py +++ b/biolink/pydanticmodel.py @@ -1167,9 +1167,9 @@ class RetrievalSource(InformationContentEntity): """ Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved. """ - resource: str = Field(None, description="""The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") + resource_id: str = Field(None, description="""The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") resource_role: ResourceRoleEnum = Field(None, description="""The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge.""") - upstream_resources: Optional[str] = Field(None, description="""The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") + upstream_resource_ids: Optional[str] = Field(None, description="""The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -3877,6 +3877,17 @@ class Association(Entity): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:Association"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3907,6 +3918,17 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalEntityAssessesNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3939,6 +3961,17 @@ class ContributorAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ContributorAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3971,6 +4004,17 @@ class GenotypeToGenotypePartAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GenotypeToGenotypePartAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4003,6 +4047,17 @@ class GenotypeToGeneAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GenotypeToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4035,6 +4090,17 @@ class GenotypeToVariantAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GenotypeToVariantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4067,6 +4133,17 @@ class GeneToGeneAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4099,6 +4176,17 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToGeneHomologyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4131,6 +4219,17 @@ class GeneToGeneFamilyAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToGeneFamilyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4178,6 +4277,17 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToGeneCoexpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4210,6 +4320,17 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:PairwiseGeneToGeneInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4243,6 +4364,17 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""identifier for the interaction. This may come from an interaction database such as IMEX.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:PairwiseMolecularInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4315,6 +4447,17 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalToChemicalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4348,6 +4491,17 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ReactionToParticipantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4381,6 +4535,17 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ReactionToCatalystAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4421,6 +4586,17 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalToChemicalDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4453,6 +4629,17 @@ class MolecularActivityToPathwayAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MolecularActivityToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4485,6 +4672,17 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4515,6 +4713,17 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4555,6 +4764,17 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalGeneInteractionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4600,6 +4820,17 @@ class ChemicalAffectsGeneAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalAffectsGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4632,6 +4863,17 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:DrugToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4672,6 +4914,17 @@ class MaterialSampleDerivationAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MaterialSampleDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4718,6 +4971,17 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:DiseaseToExposureEventAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4760,6 +5024,17 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ExposureEventToOutcomeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4823,6 +5098,17 @@ class InformationContentEntityToNamedThingAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:InformationContentEntityToNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4871,6 +5157,17 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4903,6 +5200,17 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4941,6 +5249,17 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4973,6 +5292,17 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5006,6 +5336,17 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5039,6 +5380,17 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5071,6 +5423,17 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5110,6 +5473,17 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GenotypeToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5150,6 +5524,17 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ExposureEventToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5190,6 +5575,17 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:DiseaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5230,6 +5626,17 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:CaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5270,6 +5677,17 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:BehaviorToBehavioralFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5315,6 +5733,17 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5352,6 +5781,17 @@ class GeneToPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, EntityToP original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5389,6 +5829,17 @@ class GeneToDiseaseAssociation(GeneToEntityAssociationMixin, EntityToDiseaseAsso original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5422,6 +5873,17 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:DruggableGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5457,6 +5919,17 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:VariantToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5493,6 +5966,17 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:VariantToGeneExpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5530,6 +6014,17 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:VariantToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5562,6 +6057,17 @@ class PopulationToPopulationAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:PopulationToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5593,6 +6099,17 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:VariantToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5630,6 +6147,17 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:VariantToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5663,6 +6191,17 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GenotypeToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5704,6 +6243,17 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5737,6 +6287,17 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:VariantAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5770,6 +6331,17 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GenotypeAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5803,6 +6375,17 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:CellLineAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5836,6 +6419,17 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:OrganismalEntityAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5869,6 +6463,17 @@ class OrganismToOrganismAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:OrganismToOrganismAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5899,6 +6504,17 @@ class TaxonToTaxonAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:TaxonToTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5930,6 +6546,17 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneHasVariantThatContributesToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5967,6 +6594,17 @@ class GeneToExpressionSiteAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToExpressionSiteAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -5999,6 +6637,17 @@ class SequenceVariantModulatesTreatmentAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:SequenceVariantModulatesTreatmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6031,6 +6680,17 @@ class FunctionalAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:FunctionalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6071,6 +6731,17 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MacromolecularMachineToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6103,6 +6774,17 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MacromolecularMachineToBiologicalProcessAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6135,6 +6817,17 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MacromolecularMachineToCellularComponentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6167,6 +6860,17 @@ class MolecularActivityToChemicalEntityAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MolecularActivityToChemicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6199,6 +6903,17 @@ class MolecularActivityToMolecularActivityAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:MolecularActivityToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6229,6 +6944,17 @@ class GeneToGoTermAssociation(FunctionalAssociation): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToGoTermAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6260,6 +6986,17 @@ class EntityToDiseaseAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:EntityToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6291,6 +7028,17 @@ class EntityToPhenotypicFeatureAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:EntityToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6323,6 +7071,17 @@ class SequenceAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:SequenceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6360,6 +7119,17 @@ class GenomicSequenceLocalization(SequenceAssociation): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GenomicSequenceLocalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6392,6 +7162,17 @@ class SequenceFeatureRelationship(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:SequenceFeatureRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6424,6 +7205,17 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:TranscriptToGeneRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6456,6 +7248,17 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:GeneToGeneProductRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6488,6 +7291,17 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ExonToTranscriptRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6521,6 +7335,17 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6551,6 +7376,17 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6583,6 +7419,17 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6615,6 +7462,17 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6655,6 +7513,17 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:OrganismTaxonToOrganismTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6687,6 +7556,17 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:OrganismTaxonToOrganismTaxonSpecialization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6720,6 +7600,17 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:OrganismTaxonToOrganismTaxonInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -6750,6 +7641,17 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: Optional[List[str]] = Field(["biolink:OrganismTaxonToEnvironmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. diff --git a/context.jsonld b/context.jsonld index a9ed17107c..78253c8fb1 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2023-03-30T15:48:40\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.2.5\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2023-04-03T20:55:55\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.2.5\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "AGRKB": "https://www.alliancegenome.org/", "APO": { @@ -1354,6 +1354,12 @@ "@type": "@id", "@id": "rdf:object" }, + "object_category": { + "@type": "@id" + }, + "object_category_closure": { + "@type": "@id" + }, "object_direction_qualifier": { "@context": { "@vocab": "@null", @@ -1525,7 +1531,7 @@ "resistance_associated_with": { "@type": "@id" }, - "resource": { + "resource_id": { "@type": "@id" }, "resource_role": { @@ -1545,6 +1551,9 @@ "response_increased_by": { "@type": "@id" }, + "retrieval_source_ids": { + "@type": "@id" + }, "retrieved_on": { "@type": "xsd:date" }, @@ -1613,6 +1622,12 @@ "@type": "@id", "@id": "rdf:subject" }, + "subject_category": { + "@type": "@id" + }, + "subject_category_closure": { + "@type": "@id" + }, "subject_direction_qualifier": { "@context": { "@vocab": "@null", @@ -1696,7 +1711,7 @@ "update_date": { "@type": "xsd:date" }, - "upstream_resources": { + "upstream_resource_ids": { "@type": "@id" }, "variant_part_of": { diff --git a/contextn.jsonld b/contextn.jsonld index 7af13b17fb..5dbc5f642a 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2023-03-30T15:48:45\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.2.5\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2023-04-03T20:56:00\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.2.5\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "AGRKB": "https://www.alliancegenome.org/", "APO": { @@ -1336,6 +1336,12 @@ "object": { "@type": "@id" }, + "object_category": { + "@type": "@id" + }, + "object_category_closure": { + "@type": "@id" + }, "object_direction_qualifier": { "@context": { "@vocab": "@null", @@ -1503,7 +1509,7 @@ "resistance_associated_with": { "@type": "@id" }, - "resource": { + "resource_id": { "@type": "@id" }, "resource_role": { @@ -1523,6 +1529,9 @@ "response_increased_by": { "@type": "@id" }, + "retrieval_source_ids": { + "@type": "@id" + }, "retrieved_on": { "@type": "xsd:date" }, @@ -1587,6 +1596,12 @@ "subject": { "@type": "@id" }, + "subject_category": { + "@type": "@id" + }, + "subject_category_closure": { + "@type": "@id" + }, "subject_direction_qualifier": { "@context": { "@vocab": "@null", @@ -1664,7 +1679,7 @@ "update_date": { "@type": "xsd:date" }, - "upstream_resources": { + "upstream_resource_ids": { "@type": "@id" }, "variant_part_of": { diff --git a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml index 8f3a49d772..276a7872fb 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml @@ -79,6 +79,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml index 35e05a710e..a25277eedd 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/association_config.yaml b/golr-views/association_config.yaml index 074cc9fbe5..5c1bc1bb6b 100644 --- a/golr-views/association_config.yaml +++ b/golr-views/association_config.yaml @@ -89,6 +89,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/behavior_to_behavioral_feature_association_config.yaml b/golr-views/behavior_to_behavioral_feature_association_config.yaml index b1b483bc58..5b6f734e42 100644 --- a/golr-views/behavior_to_behavioral_feature_association_config.yaml +++ b/golr-views/behavior_to_behavioral_feature_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/case_to_phenotypic_feature_association_config.yaml b/golr-views/case_to_phenotypic_feature_association_config.yaml index 8a3283f1a5..f877d065b9 100644 --- a/golr-views/case_to_phenotypic_feature_association_config.yaml +++ b/golr-views/case_to_phenotypic_feature_association_config.yaml @@ -90,6 +90,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml index 8b53339465..c06e0a54ab 100644 --- a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml +++ b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml @@ -84,6 +84,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml index 50bbd94487..e234bdb223 100644 --- a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml @@ -86,6 +86,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_affects_gene_association_config.yaml b/golr-views/chemical_affects_gene_association_config.yaml index 1c68ff6c1e..ed7d048f92 100644 --- a/golr-views/chemical_affects_gene_association_config.yaml +++ b/golr-views/chemical_affects_gene_association_config.yaml @@ -78,6 +78,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_entity_assesses_named_thing_association_config.yaml b/golr-views/chemical_entity_assesses_named_thing_association_config.yaml index 094cf077ec..5dc6ed959a 100644 --- a/golr-views/chemical_entity_assesses_named_thing_association_config.yaml +++ b/golr-views/chemical_entity_assesses_named_thing_association_config.yaml @@ -76,6 +76,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml b/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml index 757c12591e..4cc5044974 100644 --- a/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml +++ b/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml @@ -77,6 +77,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_gene_interaction_association_config.yaml b/golr-views/chemical_gene_interaction_association_config.yaml index 937bb9444f..20f950b40e 100644 --- a/golr-views/chemical_gene_interaction_association_config.yaml +++ b/golr-views/chemical_gene_interaction_association_config.yaml @@ -81,6 +81,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml index 559a8f2063..aa3c19f3db 100644 --- a/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml @@ -89,6 +89,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml index 6820d14022..1b392657cc 100644 --- a/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml @@ -88,6 +88,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_to_chemical_association_config.yaml b/golr-views/chemical_to_chemical_association_config.yaml index 6aa30cf544..495840cc27 100644 --- a/golr-views/chemical_to_chemical_association_config.yaml +++ b/golr-views/chemical_to_chemical_association_config.yaml @@ -86,6 +86,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_to_chemical_derivation_association_config.yaml b/golr-views/chemical_to_chemical_derivation_association_config.yaml index e5afa7acf2..5ccf3f466b 100644 --- a/golr-views/chemical_to_chemical_derivation_association_config.yaml +++ b/golr-views/chemical_to_chemical_derivation_association_config.yaml @@ -81,6 +81,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml index 7dba795bb4..2106a5039e 100644 --- a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml @@ -86,6 +86,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/chemical_to_pathway_association_config.yaml b/golr-views/chemical_to_pathway_association_config.yaml index d153af138a..4dbd3e42bd 100644 --- a/golr-views/chemical_to_pathway_association_config.yaml +++ b/golr-views/chemical_to_pathway_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/contributor_association_config.yaml b/golr-views/contributor_association_config.yaml index a966323388..3ad98fb2ff 100644 --- a/golr-views/contributor_association_config.yaml +++ b/golr-views/contributor_association_config.yaml @@ -73,6 +73,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml b/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml index d26fecc9b9..e72788631d 100644 --- a/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml index ee12dbf580..8a6e9a6a4d 100644 --- a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml @@ -86,6 +86,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/disease_to_exposure_event_association_config.yaml b/golr-views/disease_to_exposure_event_association_config.yaml index 24b0fa979f..0ec87c96bb 100644 --- a/golr-views/disease_to_exposure_event_association_config.yaml +++ b/golr-views/disease_to_exposure_event_association_config.yaml @@ -89,6 +89,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/disease_to_phenotypic_feature_association_config.yaml b/golr-views/disease_to_phenotypic_feature_association_config.yaml index e727674b14..cf77a16c93 100644 --- a/golr-views/disease_to_phenotypic_feature_association_config.yaml +++ b/golr-views/disease_to_phenotypic_feature_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/drug_to_gene_association_config.yaml b/golr-views/drug_to_gene_association_config.yaml index 7a6200ccb8..e1bb89037b 100644 --- a/golr-views/drug_to_gene_association_config.yaml +++ b/golr-views/drug_to_gene_association_config.yaml @@ -85,6 +85,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/druggable_gene_to_disease_association_config.yaml b/golr-views/druggable_gene_to_disease_association_config.yaml index 4c74d11f73..147cd85f5e 100644 --- a/golr-views/druggable_gene_to_disease_association_config.yaml +++ b/golr-views/druggable_gene_to_disease_association_config.yaml @@ -72,6 +72,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/entity_to_disease_association_config.yaml b/golr-views/entity_to_disease_association_config.yaml index 9214b3d57a..6ad27c0497 100644 --- a/golr-views/entity_to_disease_association_config.yaml +++ b/golr-views/entity_to_disease_association_config.yaml @@ -88,6 +88,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/entity_to_phenotypic_feature_association_config.yaml b/golr-views/entity_to_phenotypic_feature_association_config.yaml index 4853130140..44a7251f1a 100644 --- a/golr-views/entity_to_phenotypic_feature_association_config.yaml +++ b/golr-views/entity_to_phenotypic_feature_association_config.yaml @@ -88,6 +88,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/exon_to_transcript_relationship_config.yaml b/golr-views/exon_to_transcript_relationship_config.yaml index c0bd7f7544..b8ba42fa62 100644 --- a/golr-views/exon_to_transcript_relationship_config.yaml +++ b/golr-views/exon_to_transcript_relationship_config.yaml @@ -81,6 +81,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/exposure_event_to_outcome_association_config.yaml b/golr-views/exposure_event_to_outcome_association_config.yaml index 8b62acf76f..c6e6da9b8b 100644 --- a/golr-views/exposure_event_to_outcome_association_config.yaml +++ b/golr-views/exposure_event_to_outcome_association_config.yaml @@ -89,6 +89,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml index 1527327f02..045a1fb418 100644 --- a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml +++ b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml @@ -86,6 +86,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/functional_association_config.yaml b/golr-views/functional_association_config.yaml index 95ac5eecf4..9295dd8110 100644 --- a/golr-views/functional_association_config.yaml +++ b/golr-views/functional_association_config.yaml @@ -83,6 +83,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_as_a_model_of_disease_association_config.yaml b/golr-views/gene_as_a_model_of_disease_association_config.yaml index a45d7ea1a6..89549811be 100644 --- a/golr-views/gene_as_a_model_of_disease_association_config.yaml +++ b/golr-views/gene_as_a_model_of_disease_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml index f53840ef61..a282397a82 100644 --- a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml +++ b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml @@ -76,6 +76,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_disease_association_config.yaml b/golr-views/gene_to_disease_association_config.yaml index e106cfad2a..9f98fe31e8 100644 --- a/golr-views/gene_to_disease_association_config.yaml +++ b/golr-views/gene_to_disease_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_expression_site_association_config.yaml b/golr-views/gene_to_expression_site_association_config.yaml index 9ff7d3a26c..fafbc08f56 100644 --- a/golr-views/gene_to_expression_site_association_config.yaml +++ b/golr-views/gene_to_expression_site_association_config.yaml @@ -78,6 +78,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_gene_coexpression_association_config.yaml b/golr-views/gene_to_gene_coexpression_association_config.yaml index 229d7c4d24..9171ddd055 100644 --- a/golr-views/gene_to_gene_coexpression_association_config.yaml +++ b/golr-views/gene_to_gene_coexpression_association_config.yaml @@ -77,6 +77,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_gene_family_association_config.yaml b/golr-views/gene_to_gene_family_association_config.yaml index 1b18dabcf5..e8d331e077 100644 --- a/golr-views/gene_to_gene_family_association_config.yaml +++ b/golr-views/gene_to_gene_family_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_gene_homology_association_config.yaml b/golr-views/gene_to_gene_homology_association_config.yaml index b71e67a0b3..5b2a639da5 100644 --- a/golr-views/gene_to_gene_homology_association_config.yaml +++ b/golr-views/gene_to_gene_homology_association_config.yaml @@ -79,6 +79,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_gene_product_relationship_config.yaml b/golr-views/gene_to_gene_product_relationship_config.yaml index c98c8bb1d8..14680eaef2 100644 --- a/golr-views/gene_to_gene_product_relationship_config.yaml +++ b/golr-views/gene_to_gene_product_relationship_config.yaml @@ -77,6 +77,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_go_term_association_config.yaml b/golr-views/gene_to_go_term_association_config.yaml index b3fa3802ec..538ea72612 100644 --- a/golr-views/gene_to_go_term_association_config.yaml +++ b/golr-views/gene_to_go_term_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_pathway_association_config.yaml b/golr-views/gene_to_pathway_association_config.yaml index 07b5d623f6..0eb5659ef2 100644 --- a/golr-views/gene_to_pathway_association_config.yaml +++ b/golr-views/gene_to_pathway_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/gene_to_phenotypic_feature_association_config.yaml b/golr-views/gene_to_phenotypic_feature_association_config.yaml index 00c8069282..86ddc1c9fb 100644 --- a/golr-views/gene_to_phenotypic_feature_association_config.yaml +++ b/golr-views/gene_to_phenotypic_feature_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/genomic_sequence_localization_config.yaml b/golr-views/genomic_sequence_localization_config.yaml index a0b9a8a818..7238caed94 100644 --- a/golr-views/genomic_sequence_localization_config.yaml +++ b/golr-views/genomic_sequence_localization_config.yaml @@ -79,6 +79,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/genotype_as_a_model_of_disease_association_config.yaml b/golr-views/genotype_as_a_model_of_disease_association_config.yaml index a67a52f766..68be47b3b4 100644 --- a/golr-views/genotype_as_a_model_of_disease_association_config.yaml +++ b/golr-views/genotype_as_a_model_of_disease_association_config.yaml @@ -76,6 +76,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/genotype_to_disease_association_config.yaml b/golr-views/genotype_to_disease_association_config.yaml index 722986d6ed..862986439c 100644 --- a/golr-views/genotype_to_disease_association_config.yaml +++ b/golr-views/genotype_to_disease_association_config.yaml @@ -76,6 +76,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/genotype_to_gene_association_config.yaml b/golr-views/genotype_to_gene_association_config.yaml index 1aef35315f..541af37608 100644 --- a/golr-views/genotype_to_gene_association_config.yaml +++ b/golr-views/genotype_to_gene_association_config.yaml @@ -78,6 +78,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/genotype_to_genotype_part_association_config.yaml b/golr-views/genotype_to_genotype_part_association_config.yaml index ca615f809f..c60e2319bb 100644 --- a/golr-views/genotype_to_genotype_part_association_config.yaml +++ b/golr-views/genotype_to_genotype_part_association_config.yaml @@ -78,6 +78,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/genotype_to_phenotypic_feature_association_config.yaml b/golr-views/genotype_to_phenotypic_feature_association_config.yaml index 525c9b9bb3..7546ca1989 100644 --- a/golr-views/genotype_to_phenotypic_feature_association_config.yaml +++ b/golr-views/genotype_to_phenotypic_feature_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/genotype_to_variant_association_config.yaml b/golr-views/genotype_to_variant_association_config.yaml index f82f2f02f9..c573fcfa66 100644 --- a/golr-views/genotype_to_variant_association_config.yaml +++ b/golr-views/genotype_to_variant_association_config.yaml @@ -77,6 +77,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/information_content_entity_to_named_thing_association_config.yaml b/golr-views/information_content_entity_to_named_thing_association_config.yaml index d8ad6ae609..56976465bd 100644 --- a/golr-views/information_content_entity_to_named_thing_association_config.yaml +++ b/golr-views/information_content_entity_to_named_thing_association_config.yaml @@ -84,6 +84,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml index 943c63c0c4..90c6ed85ed 100644 --- a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml +++ b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml @@ -84,6 +84,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml index c94ded0eb7..5cc530eb1f 100644 --- a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml +++ b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml @@ -83,6 +83,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml index ce56095218..d4ae1da782 100644 --- a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml +++ b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml @@ -84,6 +84,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/material_sample_derivation_association_config.yaml b/golr-views/material_sample_derivation_association_config.yaml index 5ff3e4b61a..7894839747 100644 --- a/golr-views/material_sample_derivation_association_config.yaml +++ b/golr-views/material_sample_derivation_association_config.yaml @@ -78,6 +78,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml index 2fa4b8be1a..861b64a228 100644 --- a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml @@ -89,6 +89,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml index e4192cbfeb..d0c5485453 100644 --- a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml +++ b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml @@ -83,6 +83,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml index ef606ced3d..1878774370 100644 --- a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml +++ b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml @@ -83,6 +83,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/molecular_activity_to_pathway_association_config.yaml b/golr-views/molecular_activity_to_pathway_association_config.yaml index e3ca3178e9..01386fbe92 100644 --- a/golr-views/molecular_activity_to_pathway_association_config.yaml +++ b/golr-views/molecular_activity_to_pathway_association_config.yaml @@ -78,6 +78,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml b/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml index 488108396e..c56b428f69 100644 --- a/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml +++ b/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml @@ -85,6 +85,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml index f21c4f408d..c31531675e 100644 --- a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml index 17f9c78c8e..eeb6087c1f 100644 --- a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml @@ -78,6 +78,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/organism_to_organism_association_config.yaml b/golr-views/organism_to_organism_association_config.yaml index 585b6bd6bd..27366215ff 100644 --- a/golr-views/organism_to_organism_association_config.yaml +++ b/golr-views/organism_to_organism_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml index 70b7855c77..214b8c81f2 100644 --- a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml +++ b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml @@ -84,6 +84,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/pairwise_gene_to_gene_interaction_config.yaml b/golr-views/pairwise_gene_to_gene_interaction_config.yaml index 2493c8c6a1..e65efad68e 100644 --- a/golr-views/pairwise_gene_to_gene_interaction_config.yaml +++ b/golr-views/pairwise_gene_to_gene_interaction_config.yaml @@ -79,6 +79,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/pairwise_molecular_interaction_config.yaml b/golr-views/pairwise_molecular_interaction_config.yaml index 46475df807..fab20cc9ed 100644 --- a/golr-views/pairwise_molecular_interaction_config.yaml +++ b/golr-views/pairwise_molecular_interaction_config.yaml @@ -73,6 +73,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/population_to_population_association_config.yaml b/golr-views/population_to_population_association_config.yaml index b4f9de28b7..b564df67cc 100644 --- a/golr-views/population_to_population_association_config.yaml +++ b/golr-views/population_to_population_association_config.yaml @@ -77,6 +77,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/reaction_to_catalyst_association_config.yaml b/golr-views/reaction_to_catalyst_association_config.yaml index 528cd934c6..f85cc56577 100644 --- a/golr-views/reaction_to_catalyst_association_config.yaml +++ b/golr-views/reaction_to_catalyst_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/reaction_to_participant_association_config.yaml b/golr-views/reaction_to_participant_association_config.yaml index de2456b2e9..928fa4627f 100644 --- a/golr-views/reaction_to_participant_association_config.yaml +++ b/golr-views/reaction_to_participant_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/retrieval_source_config.yaml b/golr-views/retrieval_source_config.yaml index 229729e2b0..f8c1d44a6f 100644 --- a/golr-views/retrieval_source_config.yaml +++ b/golr-views/retrieval_source_config.yaml @@ -59,19 +59,19 @@ fields: description: date on which an entity was created. This can be applied to nodes or edges display_name: creation date -- id: resource +- id: resource_id description: The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge. - display_name: retrieval source_resource + display_name: retrieval source_resource id - id: resource_role description: The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge. display_name: retrieval source_resource role -- id: upstream_resources +- id: upstream_resource_ids description: The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge. - display_name: retrieval source_upstream resources + display_name: retrieval source_upstream resource ids - id: xref description: Alternate CURIEs for a thing display_name: xref diff --git a/golr-views/sequence_association_config.yaml b/golr-views/sequence_association_config.yaml index a15e325911..9c54ec38d5 100644 --- a/golr-views/sequence_association_config.yaml +++ b/golr-views/sequence_association_config.yaml @@ -90,6 +90,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/sequence_feature_relationship_config.yaml b/golr-views/sequence_feature_relationship_config.yaml index 4bdf34a82b..3c32f5abe3 100644 --- a/golr-views/sequence_feature_relationship_config.yaml +++ b/golr-views/sequence_feature_relationship_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/taxon_to_taxon_association_config.yaml b/golr-views/taxon_to_taxon_association_config.yaml index 7fc8dea8c3..1b416fcc64 100644 --- a/golr-views/taxon_to_taxon_association_config.yaml +++ b/golr-views/taxon_to_taxon_association_config.yaml @@ -80,6 +80,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/transcript_to_gene_relationship_config.yaml b/golr-views/transcript_to_gene_relationship_config.yaml index ccc8bf898b..81909589d4 100644 --- a/golr-views/transcript_to_gene_relationship_config.yaml +++ b/golr-views/transcript_to_gene_relationship_config.yaml @@ -81,6 +81,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/variant_as_a_model_of_disease_association_config.yaml b/golr-views/variant_as_a_model_of_disease_association_config.yaml index b2651e2413..0efebb6ddb 100644 --- a/golr-views/variant_as_a_model_of_disease_association_config.yaml +++ b/golr-views/variant_as_a_model_of_disease_association_config.yaml @@ -76,6 +76,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/variant_to_disease_association_config.yaml b/golr-views/variant_to_disease_association_config.yaml index 42c51b0793..731b9b9e75 100644 --- a/golr-views/variant_to_disease_association_config.yaml +++ b/golr-views/variant_to_disease_association_config.yaml @@ -76,6 +76,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/variant_to_gene_association_config.yaml b/golr-views/variant_to_gene_association_config.yaml index bd266c99e1..0cb3e33a2e 100644 --- a/golr-views/variant_to_gene_association_config.yaml +++ b/golr-views/variant_to_gene_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/variant_to_gene_expression_association_config.yaml b/golr-views/variant_to_gene_expression_association_config.yaml index 75d46c5609..ef493a1ccf 100644 --- a/golr-views/variant_to_gene_expression_association_config.yaml +++ b/golr-views/variant_to_gene_expression_association_config.yaml @@ -81,6 +81,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/variant_to_phenotypic_feature_association_config.yaml b/golr-views/variant_to_phenotypic_feature_association_config.yaml index 95901d3265..970c3aaa52 100644 --- a/golr-views/variant_to_phenotypic_feature_association_config.yaml +++ b/golr-views/variant_to_phenotypic_feature_association_config.yaml @@ -84,6 +84,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/golr-views/variant_to_population_association_config.yaml b/golr-views/variant_to_population_association_config.yaml index 853f6a64ad..95c27696b4 100644 --- a/golr-views/variant_to_population_association_config.yaml +++ b/golr-views/variant_to_population_association_config.yaml @@ -82,6 +82,63 @@ fields: an external knowledge source uses before transformation to match the biolink-model specification. display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi - id: type description: rdf:type of biolink:Association should be fixed at rdf:Statement display_name: association_type diff --git a/graphviz/anatomical_entity_to_anatomical_entity_association.gv b/graphviz/anatomical_entity_to_anatomical_entity_association.gv index 358f583f4c..c5c65e9abd 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_association.gv +++ b/graphviz/anatomical_entity_to_anatomical_entity_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "anatomical entity to anatomical entity association" [height=0.5, label="anatomical entity to anatomical entity association", - pos="1542.4,265", + pos="2492.4,265", width=6.7341]; association [height=0.5, pos="62.394,178", width=1.7332]; "anatomical entity to anatomical entity association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1300.6,263.38 988.24,261.53 461.64,254.57 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2251.1,263.25 1715.5,261.14 459.47,253.62 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1304.8,261.34 1021.7,257.37 565.81,248.19 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,\ -194.16 219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2252.2,262.49 1739.8,258.91 571.7,248.7 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "anatomical entity to anatomical entity association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1309.8,259.91 1056.2,254.76 666.73,244.65 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,\ -194.19 324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2253,262.09 1762.8,257.84 676.4,246.57 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,194.18 \ +325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "anatomical entity to anatomical entity association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1309.4,259.98 1079.8,255.15 745.19,245.56 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2252.5,262.4 1781.1,258.83 766.07,248.94 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1307.8,260.34 1105.7,256.02 829.94,247 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2251.4,262.95 1800.8,260.44 862.67,252.44 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "anatomical entity to anatomical entity association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1319,257.93 1156.9,252.49 952.08,243.14 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2252.4,262.33 1833.1,258.9 999.15,249.58 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "anatomical entity to anatomical entity association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1320,257.77 1230.8,252.91 1127.3,244.28 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2249.7,264.77 1898.7,264.75 1266.5,260.15 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "anatomical entity to anatomical entity association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1364.3,252.75 1303.2,247.41 1234.5,239.76 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2251.2,263.02 1932.7,260.76 1389.3,253.35 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "anatomical entity to anatomical entity association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1408.6,249.95 1369.3,244.66 1326.4,237.75 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2251.4,263.05 1962.5,260.81 1495.9,253.39 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "anatomical entity to anatomical entity association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1461.7,247.96 1439.6,242.75 1415.9,236.38 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2251.6,262.88 1994,260.43 1602.8,252.77 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461.1,195.6 1522,246.8 1506.7,233.96 1485.7,216.27 1468.9,202.19", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2254.7,261.42 2035.5,257.79 1726.3,249.19 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.7,246.95 1579,241.56 1587.8,235.35 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2250.2,264.12 2067,262.08 1831.5,254.31 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1651.4,248.91 1681.8,243.69 1714.6,237.07 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2267.1,258.36 2097.2,252.96 1891.1,243.48 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,8 +140,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.5,195.15 1717.3,252.51 1828.9,244.77 1957.3,234.92 1983.4,229 2013.2,222.24 2045.2,209.99 2070,199.31", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2268.4,258.07 2176.8,253.28 2088.8,244.63 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -150,9 +150,8 @@ digraph { width=1.5346]; "anatomical entity to anatomical entity association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.74 1710.4,252.01 1738.5,250.2 1767.2,248.45 1794.4,247 1844.8,244.3 2202.5,249.95 2248.4,229 2260.4,223.51 2270.8,213.39 \ -2278.8,203.69", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2348.6,250.43 2325,245.38 2305.6,238.47 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -161,9 +160,8 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.21 1709.4,251.92 1737.8,250.1 1766.9,248.38 1794.4,247 1855.2,243.95 2285,249.56 2342.4,229 2351.2,225.84 2368.1,212.71 \ -2382.5,200.7", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2397.2,248.35 2388.3,243.45 2380.5,237.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -172,85 +170,202 @@ digraph { width=1.5887]; "anatomical entity to anatomical entity association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.23 1708.1,251.85 1736.8,250.02 1766.5,248.31 1794.4,247 1832.5,245.21 2447.2,245.99 2481.4,229 2492.1,223.7 2500.8,\ -214.07 2507.4,204.67", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.98 1707.4,251.78 1736.4,249.95 1766.2,248.25 1794.4,247 1817.6,245.97 2611,241.74 2630.4,229 2638.5,223.67 2643.8,214.68 \ -2647.3,205.78", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2590.7,248.54 2601.6,243.65 2611.9,237.29 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "anatomical entity to anatomical entity association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2653.2,251.48 2689.6,246.29 2722,239.05 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "anatomical entity to anatomical entity association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.4,195.77 2667.4,252.52 2758.7,245.72 2855.4,236.92 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "anatomical entity to anatomical entity association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.17 2664.9,252.33 2691.5,250.54 2718.7,248.72 2744.4,247 2804.8,242.96 2960.5,252.45 3016.4,229 3030.2,223.21 3042.9,\ +212.57 3052.7,202.58", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "anatomical entity to anatomical entity association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.32 2661.1,252.07 2688.9,250.26 2717.5,248.5 2744.4,247 2767,245.74 3133.9,242.13 3152.4,229 3160,223.63 3164.7,214.92 \ +3167.6,206.26", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "anatomical entity to anatomical entity association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.16 2659.8,251.93 2688,250.12 2717,248.39 2744.4,247 2773.5,245.52 3242.6,242.55 3268.4,229 3278.5,223.67 3286.6,214.17 \ +3292.6,204.87", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "anatomical entity to anatomical entity association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.15 2658.1,251.82 2686.8,249.99 2716.5,248.29 2744.4,247 2784.4,245.15 3429.4,248.4 3464.4,229 3473.9,223.7 3481.2,214.34 \ +3486.5,205.14", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "anatomical entity to anatomical entity association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2657,251.76 2686.1,249.92 2716.1,248.23 2744.4,247 2794.7,244.8 3606.8,252.42 3651.4,229 3661.6,223.65 3669.6,213.96 \ +3675.4,204.53", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "anatomical entity to anatomical entity association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.75 2656.4,251.74 2685.7,249.89 2715.9,248.2 2744.4,247 2773.9,245.75 3782,242.36 3808.4,229 3818.9,223.7 3827.2,214.02 \ +3833.4,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "anatomical entity to anatomical entity association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.77 2656,251.71 2685.4,249.86 2715.8,248.18 2744.4,247 2778.1,245.61 3928.2,244.02 3958.4,229 3969.1,223.67 3977.8,213.85 \ +3984.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "anatomical entity to anatomical entity association" -> "object label closure" [color=blue, + label="object label closure", + lp="4215.9,221.5", + pos="e,4160.1,195.79 2655.7,251.69 2685.2,249.83 2715.7,248.15 2744.4,247 2782.8,245.46 4093.9,245.88 4128.4,229 4139.3,223.69 4148.1,\ +213.88 4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "anatomical entity to anatomical entity association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.5,196.3 2655.7,251.65 2685.2,249.8 2715.7,248.13 2744.4,247 2787.3,245.3 4250.7,247.58 4289.4,229 4300.2,223.79 4309.2,214.18 \ +4315.9,204.76", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "anatomical entity to anatomical entity association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1706.7,251.76 1735.9,249.92 1766,248.22 1794.4,247 1820.9,245.86 2731.8,247.96 2750.4,229 2756.6,222.69 2756.6,213.65 \ -2754.2,204.99", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2655.3,251.65 2685,249.79 2715.6,248.12 2744.4,247 2768.1,246.08 4433.8,243.79 4452.4,229 4459.2,223.54 4462.6,214.92 \ +4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "anatomical entity to anatomical entity association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.86 1706.7,251.74 1735.9,249.9 1766,248.21 1794.4,247 1849.8,244.63 2741.4,250.68 2792.4,229 2804.9,223.68 2816,213.58 \ -2824.5,203.84", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2655.3,251.64 2685,249.78 2715.6,248.12 2744.4,247 2793.1,245.11 4452.2,244.59 4498.4,229 4514.6,223.53 4530.1,212.5 \ +4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "anatomical entity to anatomical entity association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.75 1706.4,251.73 1735.7,249.88 1765.9,248.2 1794.4,247 1854.8,244.46 2824.7,247.18 2882.4,229 2900.4,223.33 2918,211.74 \ -2931.5,201.15", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2655.3,251.63 2685,249.77 2715.6,248.11 2744.4,247 2847.1,243.04 4495.4,256.49 4594.4,229 4615.1,223.24 4636,211.08 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "anatomical entity to anatomical entity association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1706.3,251.7 1735.7,249.85 1765.9,248.18 1794.4,247 1859.6,244.3 2908.1,251.54 2969.4,229 3011.9,213.37 3017.1,186.96 \ -3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2655,251.64 2684.7,249.78 2715.5,248.11 2744.4,247 2798.3,244.93 4634.1,245.49 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1841.4,265", + pos="2791.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1972.4,265", + pos="2922.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "anatomical entity to anatomical entity association_subject" [color=blue, height=0.5, label="anatomical entity", - pos="2156.4,265", + pos="3106.4,265", width=2.5456]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "anatomical entity to anatomical entity association_object" [color=blue, height=0.5, label="anatomical entity", - pos="2357.4,265", + pos="3307.4,265", width=2.5456]; } diff --git a/graphviz/anatomical_entity_to_anatomical_entity_association.svg b/graphviz/anatomical_entity_to_anatomical_entity_association.svg index ca7957f572..1e9845e099 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_association.svg +++ b/graphviz/anatomical_entity_to_anatomical_entity_association.svg @@ -4,16 +4,16 @@ - + %3 - + anatomical entity to anatomical entity association - -anatomical entity to anatomical entity association + +anatomical entity to anatomical entity association @@ -24,9 +24,9 @@ anatomical entity to anatomical entity association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ anatomical entity to anatomical entity association->id - - -id + + +id @@ -50,9 +50,9 @@ anatomical entity to anatomical entity association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ anatomical entity to anatomical entity association->name - - -name + + +name @@ -76,9 +76,9 @@ anatomical entity to anatomical entity association->description - - -description + + +description @@ -89,9 +89,9 @@ anatomical entity to anatomical entity association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ anatomical entity to anatomical entity association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ anatomical entity to anatomical entity association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ anatomical entity to anatomical entity association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ anatomical entity to anatomical entity association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ anatomical entity to anatomical entity association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ anatomical entity to anatomical entity association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ anatomical entity to anatomical entity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ anatomical entity to anatomical entity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ anatomical entity to anatomical entity association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ anatomical entity to anatomical entity association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ anatomical entity to anatomical entity association->original predicate - - -original predicate + + +original predicate original object - -string + +string anatomical entity to anatomical entity association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +anatomical entity to anatomical entity association->subject category + + +subject category + + + +object category + +ontology class + + + +anatomical entity to anatomical entity association->object category + + +object category + + + +subject closure + +string + + + +anatomical entity to anatomical entity association->subject closure + + +subject closure + + + +object closure + +string + + + +anatomical entity to anatomical entity association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +anatomical entity to anatomical entity association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +anatomical entity to anatomical entity association->object category closure + + +object category closure + + + +subject namespace + +string + + + +anatomical entity to anatomical entity association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +anatomical entity to anatomical entity association->object namespace + + +object namespace + + + +subject label closure + +string + + + +anatomical entity to anatomical entity association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +anatomical entity to anatomical entity association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +anatomical entity to anatomical entity association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + anatomical entity to anatomical entity association->type - - -type + + +type - + category - -category + +category - + anatomical entity to anatomical entity association->category - - -category + + +category - + subject - -subject + +subject - + anatomical entity to anatomical entity association->subject - - -subject + + +subject - + object - -object + +object - + anatomical entity to anatomical entity association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + anatomical entity to anatomical entity association_subject - -anatomical entity + +anatomical entity - + object->relation - - + + - + anatomical entity to anatomical entity association_object - -anatomical entity + +anatomical entity diff --git a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv index f73fb1ad92..b4be8a8da7 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv +++ b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3376,283"]; + graph [bb="0,0,5108,283"]; node [label="\N"]; "anatomical entity to anatomical entity ontogenic association" [height=0.5, label="anatomical entity to anatomical entity ontogenic association", - pos="1911.4,265", + pos="2828.4,265", width=8.0701]; "anatomical entity to anatomical entity association" [height=0.5, pos="242.43,178", width=6.7341]; "anatomical entity to anatomical entity ontogenic association" -> "anatomical entity to anatomical entity association" [label=is_a, - lp="642.43,221.5", - pos="e,340.51,194.5 1620.9,264.47 1360.5,262.9 968.45,255.59 628.43,229 534.3,221.64 427.93,207.42 350.73,196.02"]; + lp="640.43,221.5", + pos="e,338.39,194.57 2538.8,263.49 2028.6,261.9 989.11,255.41 626.43,229 532.1,222.13 425.48,207.71 348.56,196.12"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> id [color=blue, label=id, - lp="760.43,221.5", - pos="e,570.41,190.01 1628.5,260.91 1341.2,256.78 916.28,247.71 753.43,229 679.56,220.51 661.1,215.79 589.43,196 586.32,195.14 583.12,\ -194.18 579.92,193.17", + lp="756.43,221.5", + pos="e,570.42,189.98 2541.6,262.14 2012.7,258.28 922.27,248.11 749.43,229 677.26,221.02 659.37,215.5 589.43,196 586.32,195.13 583.12,\ +194.17 579.92,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "anatomical entity to anatomical entity ontogenic association" -> iri [color=blue, label=iri, - lp="879.43,221.5", - pos="e,675.04,190.17 1635.1,259.43 1377.9,254.32 1013.6,244.63 871.43,229 792.32,220.3 772.58,215.53 695.43,196 692,195.13 688.47,194.16 \ -684.93,193.14", + lp="869.43,221.5", + pos="e,675.34,190.2 2542.3,261.73 2036.7,257.31 1023.4,246.4 861.43,229 786.64,220.97 768.25,214.85 695.43,196 692.05,195.13 688.57,194.16 \ +685.09,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "anatomical entity to anatomical entity ontogenic association" -> name [color=blue, label=name, - lp="983.43,221.5", - pos="e,800.43,191.25 1632.6,259.9 1400.2,255.33 1087.8,246.2 963.43,229 910.2,221.64 850.64,205.95 810.07,194.1", + lp="976.43,221.5", + pos="e,799.39,191.54 2541.2,262.29 2055.2,258.85 1108.5,249.59 956.43,229 905.29,222.08 848.28,206.51 809.17,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity ontogenic association" -> description [color=blue, label=description, - lp="1101.9,221.5", - pos="e,946.75,193.92 1628.7,260.84 1424.3,256.95 1166.5,248.28 1061.4,229 1025.2,222.35 985.66,208.91 956.3,197.64", + lp="1096.9,221.5", + pos="e,945.48,194.14 2539.2,263.22 2074.2,261.21 1197.7,254.11 1056.4,229 1021.4,222.77 983.37,209.4 955.07,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "anatomical entity to anatomical entity ontogenic association" -> "has attribute" [color=blue, label="has attribute", - lp="1244.4,221.5", - pos="e,1086.8,192.68 1638.3,258.79 1473.3,254.05 1279.5,245.21 1197.4,229 1162.2,222.05 1123.9,208.03 1096.1,196.6", + lp="1242.4,221.5", + pos="e,1086,192.82 2539.6,262.87 2105.8,260.41 1323.2,252.7 1195.4,229 1160.5,222.52 1122.6,208.39 1095.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "anatomical entity to anatomical entity ontogenic association" -> negated [color=blue, label=negated, - lp="1393.4,221.5", - pos="e,1207.8,190.35 1653,256.72 1561.5,251.7 1458,243.24 1364.4,229 1313.3,221.22 1256,205.22 1217.6,193.4", + lp="1398.4,221.5", + pos="e,1207.6,190.46 2537.9,264.1 2178.4,262.99 1587.1,256.79 1369.4,229 1316.1,222.2 1256.5,205.66 1217.2,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "anatomical entity to anatomical entity ontogenic association" -> qualifiers [color=blue, label=qualifiers, - lp="1521.9,221.5", - pos="e,1355.4,193.25 1685.9,253.62 1621.7,248.43 1552,240.65 1488.4,229 1446.2,221.27 1399.5,207.56 1365.2,196.45", + lp="1538.9,221.5", + pos="e,1356.7,193.07 2537.9,264.08 2210,262.8 1697.2,256.26 1505.4,229 1457.6,222.2 1404.6,207.74 1366.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "anatomical entity to anatomical entity ontogenic association" -> publications [color=blue, label=publications, - lp="1653.4,221.5", - pos="e,1504.2,193.34 1735.8,250.61 1694,245.52 1649.9,238.54 1609.4,229 1576.5,221.24 1540.6,208.09 1513.7,197.22", + lp="1686.4,221.5", + pos="e,1508.2,192.71 2538.2,263.89 2243.7,262.26 1808.2,255.25 1642.4,229 1599.3,222.18 1551.8,207.69 1517.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity ontogenic association" -> "has evidence" [color=blue, label="has evidence", - lp="1784.9,221.5", - pos="e,1657.3,194.68 1813,248.05 1788.4,242.98 1762.2,236.65 1738.4,229 1713.8,221.08 1687.4,209.32 1666.5,199.19", + lp="1840.9,221.5", + pos="e,1665.9,193.61 2540.4,262.5 2285.3,259.67 1932.5,251.61 1794.4,229 1753.6,222.3 1708.7,208.48 1675.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity ontogenic association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1907.9,221.5", - pos="e,1830.8,196.34 1865.6,247.03 1857.3,242.25 1849.4,236.31 1843.4,229 1838.1,222.52 1834.8,214.16 1832.8,206.15", + lp="1995.9,221.5", + pos="e,1855.5,195.59 2554.3,259.02 2312.9,253.69 1990.6,243.94 1931.4,229 1907.9,223.07 1883.5,211.31 1864.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity ontogenic association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2090.4,221.5", - pos="e,2030.7,195.19 1941.7,247.07 1951.6,241.44 1962.5,235.06 1972.4,229 1982.8,222.63 1984.9,220.1 1995.4,214 2003.8,209.16 2012.9,\ -204.28 2021.7,199.76", + lp="2167.4,221.5", + pos="e,2062.2,196.41 2552.7,259.33 2344.2,254.5 2090.7,245.32 2072.4,229 2066.1,223.34 2063.4,214.82 2062.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity ontogenic association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2314.9,221.5", - pos="e,2253.7,194.43 2100.2,251.27 2129.3,246.07 2158.5,238.89 2185.4,229 2196.9,224.79 2197.6,219.55 2208.4,214 2219.7,208.22 2232.2,\ -202.83 2244.2,198.09", + lp="2375.9,221.5", + pos="e,2278.7,195.97 2577.8,255.88 2434.4,249.97 2280.6,240.92 2269.4,229 2262.4,221.54 2265.6,212.18 2272.1,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,8 +140,8 @@ digraph { width=1.5346]; "anatomical entity to anatomical entity ontogenic association" -> timepoint [color=blue, label=timepoint, - lp="2478.4,221.5", - pos="e,2464.5,195.15 2109.6,251.79 2249.7,242.94 2413.9,232.01 2421.4,229 2429.3,225.82 2444,213.68 2456.8,202.16", + lp="2531.4,221.5", + pos="e,2482,196.47 2629,251.85 2565.3,246.23 2508.1,238.64 2496.4,229 2489.7,223.41 2485.9,214.91 2483.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -152,9 +150,8 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "original subject" [color=blue, label="original subject", - lp="2593.4,221.5", - pos="e,2571.3,192.7 2117.8,252.33 2291.5,242.46 2512,229.79 2514.4,229 2526,225.18 2527.1,220.57 2537.4,214 2545.6,208.79 2554.5,203.21 \ -2562.7,198.07", + lp="2630.4,221.5", + pos="e,2579.7,194.92 2626.9,251.96 2602.8,246.7 2583.4,239.32 2574.4,229 2568.2,221.83 2570,212.39 2574.4,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -163,9 +160,8 @@ digraph { width=1.5887]; "anatomical entity to anatomical entity ontogenic association" -> "original predicate" [color=blue, label="original predicate", - lp="2734.9,221.5", - pos="e,2690.9,195.47 2114.3,252.07 2146.8,250.29 2180,248.53 2211.4,247 2260.1,244.62 2604.1,246.9 2649.4,229 2657.2,225.95 2671.2,213.95 \ -2683.5,202.47", + lp="2757.9,221.5", + pos="e,2696.4,195.76 2733.8,247.91 2715.6,242.88 2700.3,236.61 2694.4,229 2689.1,222.16 2689.7,213.39 2692.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -174,88 +170,205 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "original object" [color=blue, label="original object", - lp="2863.9,221.5", - pos="e,2818.6,196.41 2111.5,251.94 2144.9,250.13 2179.1,248.41 2211.4,247 2244.1,245.58 2772.3,247.28 2799.4,229 2807.3,223.68 2812.4,\ -214.86 2815.7,206.09", + lp="2876.9,221.5", + pos="e,2822.8,196.18 2827,246.8 2826.1,235.16 2824.8,219.55 2823.7,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2954.4,178", + width=2.1304]; + "anatomical entity to anatomical entity ontogenic association" -> "subject category" [color=blue, + label="subject category", + lp="3002.9,221.5", + pos="e,2950.6,196.4 2902.9,247.54 2913.6,242.83 2923.9,236.78 2932.4,229 2939.2,222.84 2944,214.24 2947.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3125.4,178", + width=2.1304]; + "anatomical entity to anatomical entity ontogenic association" -> "object category" [color=blue, + label="object category", + lp="3145.9,221.5", + pos="e,3110.6,195.73 3000.4,250.44 3023.2,245.28 3045.8,238.33 3066.4,229 3080.1,222.83 3093,212.54 3103.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3258.4,178", + width=1.0652]; + "anatomical entity to anatomical entity ontogenic association" -> "subject closure" [color=blue, + label="subject closure", + lp="3281.9,221.5", + pos="e,3246,195.51 3021.7,251.56 3105.1,245.16 3187.6,237.04 3205.4,229 3218.3,223.16 3230.1,212.86 3239.3,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3358.4,178", + width=1.0652]; + "anatomical entity to anatomical entity ontogenic association" -> "object closure" [color=blue, + label="object closure", + lp="3402.4,221.5", + pos="e,3357,196.19 3035.9,252.37 3175.1,244.16 3334.1,233.8 3340.4,229 3347.7,223.49 3352.1,214.74 3354.7,206.09", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3491.4,178", + width=2.1304]; + "anatomical entity to anatomical entity ontogenic association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3559.9,221.5", + pos="e,3484.4,196.05 3034.2,252.29 3065.7,250.51 3098,248.7 3128.4,247 3164.9,244.97 3424.5,246.74 3456.4,229 3466.2,223.59 3473.8,214.21 \ +3479.4,205.02", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3683.4,178", + width=2.1304]; + "anatomical entity to anatomical entity ontogenic association" -> "object category closure" [color=blue, + label="object category closure", + lp="3750.9,221.5", + pos="e,3677.4,196.09 3029.7,251.98 3062.7,250.18 3096.5,248.45 3128.4,247 3157.5,245.68 3626.2,243.39 3651.4,229 3660.8,223.64 3667.9,\ +214.27 3673,205.07", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3873.4,178", + width=1.0652]; + "anatomical entity to anatomical entity ontogenic association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3923.4,221.5", + pos="e,3866.4,196.17 3027.3,251.86 3061,250.05 3095.7,248.34 3128.4,247 3167.9,245.38 3803.7,247.66 3838.4,229 3848.2,223.74 3855.9,214.38 \ +3861.5,205.17", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4032.4,178", + width=1.0652]; + "anatomical entity to anatomical entity ontogenic association" -> "object namespace" [color=blue, + label="object namespace", + lp="4076.4,221.5", + pos="e,4025.1,195.72 3026.1,251.79 3060.2,249.97 3095.3,248.28 3128.4,247 3176.6,245.14 3952.6,251.13 3995.4,229 4005.8,223.66 4013.9,\ +213.98 4019.9,204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4183.4,178", + width=1.0652]; + "anatomical entity to anatomical entity ontogenic association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4236.4,221.5", + pos="e,4175.4,195.76 3025.3,251.75 3059.6,249.92 3095.1,248.24 3128.4,247 3156.6,245.95 4119.2,241.61 4144.4,229 4155.1,223.65 4163.8,\ +213.83 4170.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4354.4,178", + width=1.0652]; + "anatomical entity to anatomical entity ontogenic association" -> "object label closure" [color=blue, + label="object label closure", + lp="4401.9,221.5", + pos="e,4346.1,195.78 3024.8,251.7 3059.4,249.87 3094.9,248.2 3128.4,247 3161.4,245.82 4284.8,243.5 4314.4,229 4325.3,223.68 4334.1,213.86 \ +4340.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4507.4,178", + width=2.347]; + "anatomical entity to anatomical entity ontogenic association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4560.9,221.5", + pos="e,4501.4,196.18 3024,251.69 3058.8,249.85 3094.7,248.18 3128.4,247 3165.8,245.69 4442.7,247.18 4475.4,229 4484.9,223.74 4492,214.39 \ +4497,205.18", style=solid]; type [height=0.5, - pos="2909.4,178", + pos="4641.4,178", width=0.86659]; "anatomical entity to anatomical entity ontogenic association" -> type [color=blue, label=type, - lp="2941.4,221.5", - pos="e,2919.3,195.5 2110.3,251.86 2144,250.05 2178.7,248.34 2211.4,247 2231.1,246.19 2905.7,243.09 2919.4,229 2925.6,222.64 2925.4,213.6 \ -2922.9,204.94", + lp="4659.4,221.5", + pos="e,4644.1,195.98 3024,251.65 3058.8,249.82 3094.7,248.16 3128.4,247 3149.3,246.28 4618.7,242.82 4634.4,229 4640.9,223.32 4643.4,214.65 \ +4644.1,206.11", style=solid]; category [height=0.5, - pos="3010.4,178", + pos="4742.4,178", width=1.4263]; "anatomical entity to anatomical entity ontogenic association" -> category [color=blue, label=category, - lp="3014.9,221.5", - pos="e,2999.3,195.82 2109.9,251.84 2143.7,250.03 2178.6,248.32 2211.4,247 2253.1,245.32 2923.2,245.6 2961.4,229 2973.8,223.63 2984.6,\ -213.52 2993,203.79", + lp="4737.9,221.5", + pos="e,4727.7,195.47 3023.6,251.66 3058.5,249.82 3094.5,248.16 3128.4,247 3171.5,245.53 4638.8,243.42 4679.4,229 4694.7,223.59 4709,212.83 \ +4720.2,202.67", style=solid]; subject [height=0.5, - pos="3124.4,178", + pos="4856.4,178", width=1.2277]; "anatomical entity to anatomical entity ontogenic association" -> subject [color=blue, label=subject, - lp="3107.4,221.5", - pos="e,3107.4,194.72 2109.5,251.79 2143.5,249.98 2178.5,248.29 2211.4,247 2258,245.18 3006,243.13 3050.4,229 3068.4,223.28 3086,211.69 \ -3099.6,201.11", + lp="4833.4,221.5", + pos="e,4837.7,194.32 3023.6,251.64 3058.5,249.8 3094.5,248.15 3128.4,247 3219.8,243.91 4685.5,253.96 4773.4,229 4793.6,223.28 4813.8,\ +211.29 4829.2,200.48", style=solid]; object [height=0.5, - pos="3167.4,91", + pos="4899.4,91", width=1.0832]; "anatomical entity to anatomical entity ontogenic association" -> object [color=blue, label=object, - lp="3210.4,178", - pos="e,3180.8,108.09 2108.7,251.78 2142.9,249.95 2178.2,248.26 2211.4,247 2262.8,245.04 3089.2,246.87 3137.4,229 3179.9,213.28 3185.1,\ -186.96 3190.4,142 3191.2,135.38 3192.3,133.39 3190.4,127 3189.4,123.55 3187.9,120.13 3186.2,116.85", + lp="4943.4,178", + pos="e,4912.8,108.09 3023.6,251.63 3058.5,249.79 3094.5,248.14 3128.4,247 3176.6,245.39 4817.6,243.99 4863.4,229 4887.3,221.17 4895.4,\ +216.87 4909.4,196 4923.2,175.52 4919.5,166.51 4922.4,142 4923.2,135.38 4924.3,133.39 4922.4,127 4921.4,123.55 4919.9,120.13 4918.2,\ +116.85", style=solid]; predicate [height=0.5, - pos="3321.4,178", + pos="5053.4,178", width=1.5165]; "anatomical entity to anatomical entity ontogenic association" -> predicate [color=blue, label=predicate, - lp="3294.4,221.5", - pos="e,3297.6,194.29 2108.3,251.75 2142.6,249.93 2178.1,248.24 2211.4,247 2323.3,242.83 3109.6,255.05 3218.4,229 3243.3,223.05 3269.2,\ -210.46 3288.8,199.4", + lp="5026.4,221.5", + pos="e,5029.6,194.35 3023.2,251.63 3058.2,249.79 3094.4,248.13 3128.4,247 3229.6,243.64 4851.9,252.17 4950.4,229 4975.3,223.15 5001.2,\ +210.55 5020.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2258.4,265", + pos="3175.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2389.4,265", + pos="3306.4,265", width=2.0762]; subject -> object [label=relation, - lp="3162.4,134.5", - pos="e,3149.5,107.23 3125.5,159.55 3126.7,149.57 3129.2,137.07 3134.4,127 3136.7,122.68 3139.6,118.52 3142.8,114.66"]; + lp="4894.4,134.5", + pos="e,4881.5,107.23 4857.5,159.55 4858.7,149.57 4861.2,137.07 4866.4,127 4868.7,122.68 4871.6,118.52 4874.8,114.66"]; relation [height=0.5, - pos="3112.4,18", + pos="4844.4,18", width=1.2999]; - subject -> relation [pos="e,3113.7,36.188 3123.1,159.79 3121,132.48 3117,78.994 3114.5,46.38", + subject -> relation [pos="e,4845.7,36.188 4855.1,159.79 4853,132.48 4849,78.994 4846.5,46.38", style=dotted]; "anatomical entity to anatomical entity ontogenic association_subject" [color=blue, height=0.5, label="anatomical entity", - pos="2573.4,265", + pos="3490.4,265", width=2.5456]; - object -> relation [pos="e,3125.2,35.54 3154.9,73.889 3148,64.939 3139.2,53.617 3131.5,43.584", + object -> relation [pos="e,4857.2,35.54 4886.9,73.889 4880,64.939 4871.2,53.617 4863.5,43.584", style=dotted]; "anatomical entity to anatomical entity ontogenic association_object" [color=blue, height=0.5, label="anatomical entity", - pos="2774.4,265", + pos="3691.4,265", width=2.5456]; "anatomical entity to anatomical entity ontogenic association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2962.4,265", + pos="3879.4,265", width=2.1665]; } diff --git a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg index 947c829522..8774e1c60f 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg +++ b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg @@ -4,16 +4,16 @@ - + %3 - + anatomical entity to anatomical entity ontogenic association - -anatomical entity to anatomical entity ontogenic association + +anatomical entity to anatomical entity ontogenic association @@ -24,9 +24,9 @@ anatomical entity to anatomical entity ontogenic association->anatomical entity to anatomical entity association - - -is_a + + +is_a @@ -37,9 +37,9 @@ anatomical entity to anatomical entity ontogenic association->id - - -id + + +id @@ -50,9 +50,9 @@ anatomical entity to anatomical entity ontogenic association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ anatomical entity to anatomical entity ontogenic association->name - - -name + + +name @@ -76,9 +76,9 @@ anatomical entity to anatomical entity ontogenic association->description - - -description + + +description @@ -89,9 +89,9 @@ anatomical entity to anatomical entity ontogenic association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ anatomical entity to anatomical entity ontogenic association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ anatomical entity to anatomical entity ontogenic association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ anatomical entity to anatomical entity ontogenic association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ anatomical entity to anatomical entity ontogenic association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ anatomical entity to anatomical entity ontogenic association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ anatomical entity to anatomical entity ontogenic association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ anatomical entity to anatomical entity ontogenic association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ anatomical entity to anatomical entity ontogenic association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ anatomical entity to anatomical entity ontogenic association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ anatomical entity to anatomical entity ontogenic association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ anatomical entity to anatomical entity ontogenic association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +anatomical entity to anatomical entity ontogenic association->subject category + + +subject category + + + +object category + +ontology class + + + +anatomical entity to anatomical entity ontogenic association->object category + + +object category + + + +subject closure + +string + + + +anatomical entity to anatomical entity ontogenic association->subject closure + + +subject closure + + + +object closure + +string + + + +anatomical entity to anatomical entity ontogenic association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +anatomical entity to anatomical entity ontogenic association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +anatomical entity to anatomical entity ontogenic association->object category closure + + +object category closure + + + +subject namespace + +string + + + +anatomical entity to anatomical entity ontogenic association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +anatomical entity to anatomical entity ontogenic association->object namespace + + +object namespace + + + +subject label closure + +string + + + +anatomical entity to anatomical entity ontogenic association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +anatomical entity to anatomical entity ontogenic association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +anatomical entity to anatomical entity ontogenic association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + anatomical entity to anatomical entity ontogenic association->type - - -type + + +type - + category - -category + +category - + anatomical entity to anatomical entity ontogenic association->category - - -category + + +category - + subject - -subject + +subject - + anatomical entity to anatomical entity ontogenic association->subject - - -subject + + +subject - + object - -object + +object - + anatomical entity to anatomical entity ontogenic association->object - - -object + + +object - + predicate - -predicate + +predicate - + anatomical entity to anatomical entity ontogenic association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + anatomical entity to anatomical entity ontogenic association_subject - -anatomical entity + +anatomical entity - + object->relation - - + + - + anatomical entity to anatomical entity ontogenic association_object - -anatomical entity + +anatomical entity - + anatomical entity to anatomical entity ontogenic association_predicate - -predicate type + +predicate type diff --git a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv index f10fb8d0d8..f24adaf247 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv +++ b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3376,283"]; + graph [bb="0,0,5108,283"]; node [label="\N"]; "anatomical entity to anatomical entity part of association" [height=0.5, label="anatomical entity to anatomical entity part of association", - pos="1911.4,265", + pos="2828.4,265", width=7.6729]; "anatomical entity to anatomical entity association" [height=0.5, pos="242.43,178", width=6.7341]; "anatomical entity to anatomical entity part of association" -> "anatomical entity to anatomical entity association" [label=is_a, - lp="642.43,221.5", - pos="e,340.51,194.5 1635.1,264.55 1375,263.16 974.7,256.08 628.43,229 534.3,221.64 427.93,207.42 350.73,196.02"]; + lp="640.43,221.5", + pos="e,338.39,194.57 2553,263.53 2048.1,262.02 992.51,255.66 626.43,229 532.1,222.13 425.48,207.71 348.56,196.12"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity part of association" -> id [color=blue, label=id, - lp="760.43,221.5", - pos="e,570.41,190.01 1641.6,261.09 1354.3,257.06 918.78,248 753.43,229 679.56,220.51 661.1,215.79 589.43,196 586.32,195.14 583.12,194.18 \ -579.92,193.17", + lp="756.43,221.5", + pos="e,570.42,189.98 2555.3,262.24 2031.9,258.46 923.78,248.28 749.43,229 677.26,221.02 659.37,215.5 589.43,196 586.32,195.13 583.12,\ +194.17 579.92,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "anatomical entity to anatomical entity part of association" -> iri [color=blue, label=iri, - lp="879.43,221.5", - pos="e,675.04,190.17 1647.5,259.68 1389.8,254.63 1015.9,244.89 871.43,229 792.32,220.3 772.58,215.53 695.43,196 692,195.13 688.47,194.16 \ -684.93,193.14", + lp="869.43,221.5", + pos="e,675.34,190.2 2556,261.85 2055.4,257.51 1024.9,246.56 861.43,229 786.64,220.97 768.25,214.85 695.43,196 692.05,195.13 688.57,194.16 \ +685.09,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "anatomical entity to anatomical entity part of association" -> name [color=blue, label=name, - lp="983.43,221.5", - pos="e,800.43,191.25 1645.4,260.14 1411.8,255.66 1090.1,246.52 963.43,229 910.2,221.64 850.64,205.95 810.07,194.1", + lp="976.43,221.5", + pos="e,799.39,191.54 2555,262.39 2073.4,259.03 1110,249.79 956.43,229 905.29,222.08 848.28,206.51 809.17,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity part of association" -> description [color=blue, label=description, - lp="1101.9,221.5", - pos="e,946.75,193.92 1641.6,261.08 1435.3,257.31 1168.7,248.69 1061.4,229 1025.2,222.35 985.66,208.91 956.3,197.64", + lp="1096.9,221.5", + pos="e,945.48,194.14 2553.1,263.27 2091.9,261.35 1199.1,254.37 1056.4,229 1021.4,222.77 983.37,209.4 955.07,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "anatomical entity to anatomical entity part of association" -> "has attribute" [color=blue, label="has attribute", - lp="1244.4,221.5", - pos="e,1086.8,192.68 1650.2,259.13 1482.7,254.47 1281.5,245.6 1197.4,229 1162.2,222.05 1123.9,208.03 1096.1,196.6", + lp="1242.4,221.5", + pos="e,1086,192.82 2553.6,262.95 2123,260.57 1324.6,252.96 1195.4,229 1160.5,222.52 1122.6,208.39 1095.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "anatomical entity to anatomical entity part of association" -> negated [color=blue, label=negated, - lp="1393.4,221.5", - pos="e,1207.8,190.35 1662.3,257.22 1568.5,252.27 1461.2,243.72 1364.4,229 1313.3,221.22 1256,205.22 1217.6,193.4", + lp="1398.4,221.5", + pos="e,1207.6,190.46 2552.2,264.15 2194.3,263.16 1590.1,257.16 1369.4,229 1316.1,222.2 1256.5,205.66 1217.2,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "anatomical entity to anatomical entity part of association" -> qualifiers [color=blue, label=qualifiers, - lp="1521.9,221.5", - pos="e,1355.4,193.25 1691.6,254.08 1625.9,248.89 1553.9,241 1488.4,229 1446.2,221.27 1399.5,207.56 1365.2,196.45", + lp="1538.9,221.5", + pos="e,1356.7,193.07 2552.4,264.13 2225.3,262.99 1700,256.67 1505.4,229 1457.6,222.2 1404.6,207.74 1366.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "anatomical entity to anatomical entity part of association" -> publications [color=blue, label=publications, - lp="1653.4,221.5", - pos="e,1504.2,193.34 1738.5,250.95 1696,245.83 1650.8,238.75 1609.4,229 1576.5,221.24 1540.6,208.09 1513.7,197.22", + lp="1686.4,221.5", + pos="e,1508.2,192.71 2552.4,263.97 2257.8,262.48 1810.9,255.67 1642.4,229 1599.3,222.18 1551.8,207.69 1517.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity part of association" -> "has evidence" [color=blue, label="has evidence", - lp="1784.9,221.5", - pos="e,1657.3,194.68 1813.5,248.14 1788.7,243.06 1762.3,236.7 1738.4,229 1713.8,221.08 1687.4,209.32 1666.5,199.19", + lp="1840.9,221.5", + pos="e,1665.9,193.61 2554.5,262.66 2298.4,259.96 1935,252.03 1794.4,229 1753.6,222.3 1708.7,208.48 1675.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity part of association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1907.9,221.5", - pos="e,1830.8,196.34 1865.9,247.23 1857.5,242.42 1849.5,236.41 1843.4,229 1838.1,222.52 1834.8,214.16 1832.8,206.15", + lp="1995.9,221.5", + pos="e,1855.5,195.59 2566.4,259.29 2323.8,254.02 1991.6,244.19 1931.4,229 1907.9,223.07 1883.5,211.31 1864.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity part of association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2090.4,221.5", - pos="e,2030.7,195.19 1941.7,247.07 1951.6,241.44 1962.5,235.06 1972.4,229 1982.8,222.63 1984.9,220.1 1995.4,214 2003.8,209.16 2012.9,\ -204.28 2021.7,199.76", + lp="2167.4,221.5", + pos="e,2062.2,196.41 2564.7,259.6 2354.1,254.85 2091,245.63 2072.4,229 2066.1,223.34 2063.4,214.82 2062.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "anatomical entity to anatomical entity part of association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2314.9,221.5", - pos="e,2253.7,194.43 2098,251.66 2127.8,246.43 2157.9,239.14 2185.4,229 2196.9,224.79 2197.6,219.55 2208.4,214 2219.7,208.22 2232.2,202.83 \ -2244.2,198.09", + lp="2375.9,221.5", + pos="e,2278.7,195.97 2586.9,256.26 2441,250.36 2280.9,241.17 2269.4,229 2262.4,221.54 2265.6,212.18 2272.1,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,8 +140,8 @@ digraph { width=1.5346]; "anatomical entity to anatomical entity part of association" -> timepoint [color=blue, label=timepoint, - lp="2478.4,221.5", - pos="e,2464.5,195.15 2104.5,252.11 2245.7,243.2 2413.8,232.05 2421.4,229 2429.3,225.82 2444,213.68 2456.8,202.16", + lp="2531.4,221.5", + pos="e,2482,196.47 2633.2,252.21 2567.8,246.56 2508.3,238.85 2496.4,229 2489.7,223.41 2485.9,214.91 2483.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -152,9 +150,8 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity part of association" -> "original subject" [color=blue, label="original subject", - lp="2593.4,221.5", - pos="e,2571.3,192.7 2107.2,252.29 2137.4,250.51 2168.3,248.7 2197.4,247 2267.9,242.91 2447.4,251.02 2514.4,229 2526,225.19 2527.1,220.57 \ -2537.4,214 2545.6,208.79 2554.5,203.21 2562.7,198.07", + lp="2630.4,221.5", + pos="e,2579.7,194.92 2629.3,252.46 2604,247.18 2583.7,239.65 2574.4,229 2568.2,221.83 2570,212.39 2574.4,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -163,9 +160,8 @@ digraph { width=1.5887]; "anatomical entity to anatomical entity part of association" -> "original predicate" [color=blue, label="original predicate", - lp="2734.9,221.5", - pos="e,2690.9,195.48 2103.7,252.05 2135,250.26 2167.1,248.5 2197.4,247 2247.6,244.51 2602.7,247.44 2649.4,229 2657.2,225.95 2671.2,213.95 \ -2683.5,202.47", + lp="2757.9,221.5", + pos="e,2696.4,195.76 2734.2,248.01 2715.8,242.96 2700.3,236.66 2694.4,229 2689.1,222.16 2689.7,213.39 2692.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -174,88 +170,204 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity part of association" -> "original object" [color=blue, label="original object", - lp="2863.9,221.5", - pos="e,2818.6,196.41 2101.4,251.92 2133.4,250.11 2166.4,248.39 2197.4,247 2230.9,245.51 2771.7,247.7 2799.4,229 2807.3,223.69 2812.4,\ -214.86 2815.7,206.1", + lp="2876.9,221.5", + pos="e,2822.8,196.18 2827,246.8 2826.1,235.16 2824.8,219.55 2823.7,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2954.4,178", + width=2.1304]; + "anatomical entity to anatomical entity part of association" -> "subject category" [color=blue, + label="subject category", + lp="3002.9,221.5", + pos="e,2950.6,196.4 2902.6,247.66 2913.5,242.93 2923.9,236.84 2932.4,229 2939.2,222.84 2944,214.24 2947.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3125.4,178", + width=2.1304]; + "anatomical entity to anatomical entity part of association" -> "object category" [color=blue, + label="object category", + lp="3145.9,221.5", + pos="e,3110.6,195.73 2998.9,250.79 3022.2,245.6 3045.3,238.55 3066.4,229 3080.1,222.83 3093,212.54 3103.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3258.4,178", + width=1.0652]; + "anatomical entity to anatomical entity part of association" -> "subject closure" [color=blue, + label="subject closure", + lp="3281.9,221.5", + pos="e,3246,195.51 3017.5,251.88 3102.3,245.44 3187.3,237.18 3205.4,229 3218.3,223.16 3230.1,212.86 3239.3,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3358.4,178", + width=1.0652]; + "anatomical entity to anatomical entity part of association" -> "object closure" [color=blue, + label="object closure", + lp="3402.4,221.5", + pos="e,3357,196.19 3020.6,252.06 3164.5,242.93 3337.1,231.5 3340.4,229 3347.7,223.49 3352.1,214.74 3354.7,206.09", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3491.4,178", + width=2.1304]; + "anatomical entity to anatomical entity part of association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3560.9,221.5", + pos="e,3484.4,196.06 3023.4,252.23 3053.9,250.45 3085,248.65 3114.4,247 3152.4,244.87 3423.2,247.45 3456.4,229 3466.2,223.6 3473.8,214.22 \ +3479.4,205.03", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3683.4,178", + width=2.1304]; + "anatomical entity to anatomical entity part of association" -> "object category closure" [color=blue, + label="object category closure", + lp="3750.9,221.5", + pos="e,3677.7,196.08 3019.2,251.97 3051,250.17 3083.6,248.43 3114.4,247 3144.3,245.61 3626.5,243.98 3652.4,229 3661.6,223.68 3668.4,214.45 \ +3673.3,205.35", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3873.4,178", + width=1.0652]; + "anatomical entity to anatomical entity part of association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3923.4,221.5", + pos="e,3866.4,196.17 3017.2,251.85 3049.6,250.03 3083,248.32 3114.4,247 3154.6,245.31 3803,248.02 3838.4,229 3848.2,223.74 3855.9,214.38 \ +3861.5,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4032.4,178", + width=1.0652]; + "anatomical entity to anatomical entity part of association" -> "object namespace" [color=blue, + label="object namespace", + lp="4076.4,221.5", + pos="e,4025.1,195.73 3016.4,251.78 3049.1,249.95 3082.7,248.26 3114.4,247 3163.3,245.05 3951.9,251.48 3995.4,229 4005.8,223.66 4013.9,\ +213.98 4020,204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4183.4,178", + width=1.0652]; + "anatomical entity to anatomical entity part of association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4236.4,221.5", + pos="e,4175.4,195.76 3015.7,251.74 3048.6,249.91 3082.5,248.23 3114.4,247 3143,245.9 4118.8,241.78 4144.4,229 4155.1,223.66 4163.8,213.83 \ +4170.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4354.4,178", + width=1.0652]; + "anatomical entity to anatomical entity part of association" -> "object label closure" [color=blue, + label="object label closure", + lp="4401.9,221.5", + pos="e,4346.1,195.78 3014.9,251.72 3048,249.88 3082.2,248.2 3114.4,247 3147.7,245.76 4284.5,243.67 4314.4,229 4325.3,223.68 4334.1,213.86 \ +4340.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4507.4,178", + width=2.347]; + "anatomical entity to anatomical entity part of association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4560.9,221.5", + pos="e,4501.4,196.18 3014.5,251.69 3047.8,249.85 3082.1,248.17 3114.4,247 3152.2,245.63 4442.4,247.37 4475.4,229 4484.9,223.74 4492,214.39 \ +4497,205.18", style=solid]; type [height=0.5, - pos="2909.4,178", + pos="4641.4,178", width=0.86659]; "anatomical entity to anatomical entity part of association" -> type [color=blue, label=type, - lp="2941.4,221.5", - pos="e,2919.3,195.5 2100.2,251.85 2132.6,250.03 2166,248.33 2197.4,247 2217.5,246.15 2905.4,243.36 2919.4,229 2925.6,222.65 2925.4,213.6 \ -2922.9,204.94", + lp="4659.4,221.5", + pos="e,4644.1,195.98 3014.1,251.67 3047.5,249.83 3082,248.16 3114.4,247 3135.5,246.25 4618.6,242.95 4634.4,229 4640.9,223.32 4643.4,214.65 \ +4644.1,206.11", style=solid]; category [height=0.5, - pos="3010.4,178", + pos="4742.4,178", width=1.4263]; "anatomical entity to anatomical entity part of association" -> category [color=blue, label=category, - lp="3014.9,221.5", - pos="e,2999.4,195.83 2100.2,251.82 2132.6,250 2166,248.3 2197.4,247 2239.8,245.24 2922.5,245.91 2961.4,229 2973.8,223.63 2984.6,213.53 \ -2993,203.8", + lp="4737.9,221.5", + pos="e,4727.7,195.47 3014.1,251.67 3047.5,249.82 3082,248.15 3114.4,247 3157.9,245.46 4638.5,243.55 4679.4,229 4694.7,223.59 4709,212.83 \ +4720.2,202.68", style=solid]; subject [height=0.5, - pos="3124.4,178", + pos="4856.4,178", width=1.2277]; "anatomical entity to anatomical entity part of association" -> subject [color=blue, label=subject, - lp="3107.4,221.5", - pos="e,3107.4,194.72 2099.4,251.8 2132.1,249.97 2165.7,248.28 2197.4,247 2244.8,245.09 3005.3,243.35 3050.4,229 3068.4,223.28 3086,211.7 \ -3099.6,201.12", + lp="4833.4,221.5", + pos="e,4837.7,194.32 3014.1,251.65 3047.5,249.8 3082,248.14 3114.4,247 3206.5,243.76 4684.8,254.16 4773.4,229 4793.6,223.28 4813.8,211.29 \ +4829.2,200.48", style=solid]; object [height=0.5, - pos="3167.4,91", + pos="4899.4,91", width=1.0832]; "anatomical entity to anatomical entity part of association" -> object [color=blue, label=object, - lp="3210.4,178", - pos="e,3180.8,108.09 2099.1,251.76 2131.8,249.94 2165.6,248.25 2197.4,247 2249.6,244.95 3088.4,247.13 3137.4,229 3179.9,213.28 3185.1,\ -186.96 3190.4,142 3191.2,135.38 3192.3,133.39 3190.4,127 3189.4,123.55 3187.9,120.13 3186.2,116.85", + lp="4943.4,178", + pos="e,4912.8,108.09 3014.1,251.63 3047.5,249.79 3082,248.13 3114.4,247 3163,245.31 4817.3,244.11 4863.4,229 4887.3,221.17 4895.4,216.87 \ +4909.4,196 4923.2,175.52 4919.5,166.51 4922.4,142 4923.2,135.38 4924.3,133.39 4922.4,127 4921.4,123.55 4919.9,120.13 4918.2,116.85", style=solid]; predicate [height=0.5, - pos="3321.4,178", + pos="5053.4,178", width=1.5165]; "anatomical entity to anatomical entity part of association" -> predicate [color=blue, label=predicate, - lp="3294.4,221.5", - pos="e,3297.6,194.29 2098.7,251.75 2131.6,249.91 2165.5,248.23 2197.4,247 2310.8,242.63 3108.1,255.39 3218.4,229 3243.3,223.05 3269.2,\ -210.46 3288.8,199.4", + lp="5026.4,221.5", + pos="e,5029.6,194.35 3013.8,251.64 3047.2,249.79 3081.9,248.13 3114.4,247 3216.4,243.47 4851.1,252.34 4950.4,229 4975.3,223.15 5001.2,\ +210.56 5020.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2244.4,265", + pos="3161.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2375.4,265", + pos="3292.4,265", width=2.0762]; subject -> object [label=relation, - lp="3162.4,134.5", - pos="e,3149.5,107.23 3125.5,159.55 3126.7,149.57 3129.2,137.07 3134.4,127 3136.7,122.68 3139.6,118.52 3142.8,114.66"]; + lp="4894.4,134.5", + pos="e,4881.5,107.23 4857.5,159.55 4858.7,149.57 4861.2,137.07 4866.4,127 4868.7,122.68 4871.6,118.52 4874.8,114.66"]; relation [height=0.5, - pos="3112.4,18", + pos="4844.4,18", width=1.2999]; - subject -> relation [pos="e,3113.7,36.188 3123.1,159.79 3121,132.48 3117,78.994 3114.5,46.38", + subject -> relation [pos="e,4845.7,36.188 4855.1,159.79 4853,132.48 4849,78.994 4846.5,46.38", style=dotted]; "anatomical entity to anatomical entity part of association_subject" [color=blue, height=0.5, label="anatomical entity", - pos="2559.4,265", + pos="3476.4,265", width=2.5456]; - object -> relation [pos="e,3125.2,35.54 3154.9,73.889 3148,64.939 3139.2,53.617 3131.5,43.584", + object -> relation [pos="e,4857.2,35.54 4886.9,73.889 4880,64.939 4871.2,53.617 4863.5,43.584", style=dotted]; "anatomical entity to anatomical entity part of association_object" [color=blue, height=0.5, label="anatomical entity", - pos="2760.4,265", + pos="3677.4,265", width=2.5456]; "anatomical entity to anatomical entity part of association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2948.4,265", + pos="3865.4,265", width=2.1665]; } diff --git a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg index 5b44a4c6d0..15a5f53802 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg +++ b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg @@ -4,16 +4,16 @@ - + %3 - + anatomical entity to anatomical entity part of association - -anatomical entity to anatomical entity part of association + +anatomical entity to anatomical entity part of association @@ -24,9 +24,9 @@ anatomical entity to anatomical entity part of association->anatomical entity to anatomical entity association - - -is_a + + +is_a @@ -37,9 +37,9 @@ anatomical entity to anatomical entity part of association->id - - -id + + +id @@ -50,9 +50,9 @@ anatomical entity to anatomical entity part of association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ anatomical entity to anatomical entity part of association->name - - -name + + +name @@ -76,9 +76,9 @@ anatomical entity to anatomical entity part of association->description - - -description + + +description @@ -89,9 +89,9 @@ anatomical entity to anatomical entity part of association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ anatomical entity to anatomical entity part of association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ anatomical entity to anatomical entity part of association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ anatomical entity to anatomical entity part of association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ anatomical entity to anatomical entity part of association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ anatomical entity to anatomical entity part of association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ anatomical entity to anatomical entity part of association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ anatomical entity to anatomical entity part of association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ anatomical entity to anatomical entity part of association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ anatomical entity to anatomical entity part of association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ anatomical entity to anatomical entity part of association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ anatomical entity to anatomical entity part of association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +anatomical entity to anatomical entity part of association->subject category + + +subject category + + + +object category + +ontology class + + + +anatomical entity to anatomical entity part of association->object category + + +object category + + + +subject closure + +string + + + +anatomical entity to anatomical entity part of association->subject closure + + +subject closure + + + +object closure + +string + + + +anatomical entity to anatomical entity part of association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +anatomical entity to anatomical entity part of association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +anatomical entity to anatomical entity part of association->object category closure + + +object category closure + + + +subject namespace + +string + + + +anatomical entity to anatomical entity part of association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +anatomical entity to anatomical entity part of association->object namespace + + +object namespace + + + +subject label closure + +string + + + +anatomical entity to anatomical entity part of association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +anatomical entity to anatomical entity part of association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +anatomical entity to anatomical entity part of association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + anatomical entity to anatomical entity part of association->type - - -type + + +type - + category - -category + +category - + anatomical entity to anatomical entity part of association->category - - -category + + +category - + subject - -subject + +subject - + anatomical entity to anatomical entity part of association->subject - - -subject + + +subject - + object - -object + +object - + anatomical entity to anatomical entity part of association->object - - -object + + +object - + predicate - -predicate + +predicate - + anatomical entity to anatomical entity part of association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + anatomical entity to anatomical entity part of association_subject - -anatomical entity + +anatomical entity - + object->relation - - + + - + anatomical entity to anatomical entity part of association_object - -anatomical entity + +anatomical entity - + anatomical entity to anatomical entity part of association_predicate - -predicate type + +predicate type diff --git a/graphviz/association.gv b/graphviz/association.gv index 3132bae0f5..379f7a969f 100644 --- a/graphviz/association.gv +++ b/graphviz/association.gv @@ -1,17 +1,16 @@ digraph { - graph [bb="0,0,3140.7,283"]; + graph [bb="0,0,4830.7,283"]; node [label="\N"]; association [height=0.5, label=association, - pos="1396.3,265", + pos="2450.3,265", width=1.7332]; entity [height=0.5, pos="38.347,178", width=1.0652]; association -> entity [label=is_a, - lp="234.35,221.5", - pos="e,67.386,189.8 1333.7,263.88 1122.7,263.22 438.41,258.75 220.35,229 159.57,220.71 145.1,213.59 86.347,196 83.255,195.07 80.07,194.07 \ -76.88,193.02"]; + lp="232.35,221.5", + pos="e,67.441,189.82 2387.9,263.88 2049,263.08 438.22,257.82 218.35,229 168.52,222.47 113.08,205.53 77.063,193.17"]; id [color=blue, height=0.5, label=string, @@ -19,9 +18,9 @@ digraph { width=1.0652]; association -> id [color=blue, label=id, - lp="352.35,221.5", - pos="e,162.33,190.01 1334,263.28 1138.5,260.8 538.59,251.5 345.35,229 271.5,220.4 253.01,215.79 181.35,196 178.24,195.14 175.04,194.18 \ -171.84,193.17", + lp="348.35,221.5", + pos="e,162.33,189.98 2387.9,263.66 2060.4,261.78 548.87,251.92 341.35,229 269.18,221.03 251.29,215.5 181.35,196 178.24,195.13 175.04,\ +194.17 171.84,193.15", style=solid]; iri [color=blue, height=0.5, @@ -30,9 +29,9 @@ digraph { width=1.2277]; association -> iri [color=blue, label=iri, - lp="465.35,221.5", - pos="e,267.25,190.22 1334.1,262.94 1152.9,259.64 627.92,248.62 457.35,229 380.88,220.21 361.9,215.12 287.35,196 283.97,195.13 280.49,\ -194.17 277,193.16", + lp="455.35,221.5", + pos="e,267.26,190.16 2387.9,263.6 2070.6,261.48 643.79,250.78 447.35,229 375.18,221 357.57,214.45 287.35,196 283.97,195.11 280.5,194.14 \ +277.02,193.12", style=solid]; name [color=blue, height=0.5, @@ -41,8 +40,8 @@ digraph { width=1.5707]; association -> name [color=blue, label=name, - lp="567.35,221.5", - pos="e,391.5,191.39 1334,263.14 1164.7,260.52 699.12,251.43 547.35,229 496.81,221.53 440.4,206.17 401.5,194.44", + lp="559.35,221.5", + pos="e,390.2,191.77 2388,263.76 2079.7,262.47 725.5,255.32 539.35,229 490.87,222.15 437,206.78 399.77,194.87", style=solid]; description [color=blue, height=0.5, @@ -51,8 +50,8 @@ digraph { width=2.0943]; association -> description [color=blue, label=description, - lp="681.85,221.5", - pos="e,536.56,194.25 1334.1,263.52 1178,261.93 773.24,255.32 641.35,229 608.41,222.43 572.8,209.37 546.01,198.24", + lp="675.85,221.5", + pos="e,534.72,194.4 2387.6,264.06 2088,264.18 809.99,262.71 635.35,229 603.66,222.88 569.65,209.83 544.09,198.6", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,8 +60,8 @@ digraph { width=1.4443]; association -> "has attribute" [color=blue, label="has attribute", - lp="818.35,221.5", - pos="e,676.31,193.48 1334.2,263.12 1198,260.76 877.18,252.78 771.35,229 741.37,222.26 709.26,208.99 685.37,197.8", + lp="814.35,221.5", + pos="e,674.81,193.55 2387.9,264.09 2102.4,264.3 927.88,263.1 767.35,229 738.06,222.78 706.94,209.44 683.86,198.1", style=solid]; subject [color=blue, height=0.5, @@ -72,7 +71,7 @@ digraph { association -> subject [color=blue, label=subject, lp="941.35,221.5", - pos="e,819.08,194.15 1334.6,261.83 1223.3,257.52 993.41,246.77 915.35,229 885.26,222.15 852.92,209.33 828.41,198.39", + pos="e,818.47,194.37 2387.7,263.87 2117.7,263.13 1061,258.37 915.35,229 884.89,222.86 852.33,209.9 827.79,198.71", style=solid]; predicate [color=blue, height=0.5, @@ -82,7 +81,7 @@ digraph { association -> predicate [color=blue, label=predicate, lp="1020.3,221.5", - pos="e,960.72,196.39 1334.9,261.74 1227.7,257.35 1015.4,246.57 986.35,229 977.31,223.54 970.38,214.45 965.32,205.5", + pos="e,960.36,196.14 2387.6,264.14 2115.5,264.52 1048.2,263.8 986.35,229 976.92,223.69 969.84,214.33 964.77,205.13", style=solid]; object [color=blue, height=0.5, @@ -92,8 +91,8 @@ digraph { association -> object [color=blue, label=object, lp="1099.3,178", - pos="e,927.99,105.47 1335.2,261.24 1268.2,255.96 1159.4,240.61 1077.3,196 1057.5,185.2 1060,172.77 1041.3,160 1009.2,138.07 968.92,120.64 \ -937.45,108.92", + pos="e,927.99,105.47 2388.2,263.11 2180.1,259.97 1509.6,248.55 1294.3,229 1197.2,220.17 1164.4,240.02 1077.3,196 1057.2,185.79 1060,172.77 \ +1041.3,160 1009.2,138.07 968.92,120.64 937.45,108.92", style=solid]; negated [color=blue, height=0.5, @@ -102,8 +101,8 @@ digraph { width=1.2999]; association -> negated [color=blue, label=negated, - lp="1320.3,221.5", - pos="e,1206.1,192.48 1355.4,251.31 1335.9,245.01 1312.2,237.04 1291.3,229 1265.7,219.12 1237.4,206.72 1215.4,196.74", + lp="1404.3,221.5", + pos="e,1211.9,190.37 2388,263.56 2189.4,261.91 1573.1,254.79 1375.3,229 1321.5,221.98 1261.3,205.49 1221.6,193.36", style=solid]; qualifiers [color=blue, height=0.5, @@ -112,8 +111,8 @@ digraph { width=2.1304]; association -> qualifiers [color=blue, label=qualifiers, - lp="1395.8,221.5", - pos="e,1333.7,195.76 1380.9,247.21 1369.4,234.63 1353.4,217.25 1340.5,203.18", + lp="1537.8,221.5", + pos="e,1360.2,193.18 2387.9,263.53 2205.4,261.85 1675.5,254.83 1504.3,229 1458.1,222.01 1406.8,207.72 1369.8,196.19", style=solid]; publications [color=blue, height=0.5, @@ -122,8 +121,8 @@ digraph { width=1.7332]; association -> publications [color=blue, label=publications, - lp="1491.3,221.5", - pos="e,1462.2,195.62 1414.4,247.67 1420.6,241.91 1427.4,235.31 1433.3,229 1440.9,220.96 1448.8,211.79 1455.7,203.52", + lp="1675.3,221.5", + pos="e,1510,193.06 2388.1,263.49 2222.9,261.79 1776.4,254.87 1631.3,229 1592.7,222.11 1550.4,208.11 1519.6,196.67", style=solid]; "has evidence" [color=blue, height=0.5, @@ -132,8 +131,8 @@ digraph { width=2.0943]; association -> "has evidence" [color=blue, label="has evidence", - lp="1617.8,221.5", - pos="e,1606,195.08 1443,252.88 1482.9,243.32 1534.7,230.79 1539.3,229 1559.2,221.31 1580.2,210.17 1597.1,200.36", + lp="1821.8,221.5", + pos="e,1665.8,194.06 2388.2,263.01 2244.2,260.37 1891.6,251.72 1775.3,229 1740.8,222.26 1703.4,209.05 1675.3,197.9", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -142,9 +141,8 @@ digraph { width=3.015]; association -> "knowledge source" [color=blue, label="knowledge source", - lp="1792.8,221.5", - pos="e,1790.5,194.61 1441.1,252.4 1450.1,250.36 1459.5,248.44 1468.3,247 1556.4,232.71 1580.7,246.03 1668.3,229 1706.7,221.55 1748.8,\ -208.7 1780.9,197.89", + lp="1961.8,221.5", + pos="e,1849.2,195.93 2387.5,264.66 2262.1,265.21 1985.4,262.45 1897.3,229 1882.4,223.32 1868.1,212.85 1856.9,202.96", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -153,9 +151,8 @@ digraph { width=3.015]; association -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2031.3,221.5", - pos="e,2017.8,194.07 1440.7,252.17 1449.8,250.13 1459.3,248.26 1468.3,247 1641.5,222.81 1688.2,253.64 1861.3,229 1911.4,221.88 1967,208.1 \ -2008,196.81", + lp="2128.3,221.5", + pos="e,2045,195.58 2387.9,263.32 2277.4,261.45 2056.8,254.54 2033.3,229 2026,221.04 2030.1,211.47 2037.7,202.85", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -164,9 +161,8 @@ digraph { width=3.015]; association -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2304.8,221.5", - pos="e,2260.7,194.63 1440.3,252.13 1449.5,250.06 1459.2,248.19 1468.3,247 1760.2,208.98 1839.5,274.23 2130.3,229 2171.7,222.57 2217.1,\ -209.21 2251,197.91", + lp="2337.8,221.5", + pos="e,2254.9,194.15 2388.4,262.76 2330.9,260.15 2251.2,252.29 2231.3,229 2221.3,217.19 2230.7,206.86 2245.6,198.69", style=solid]; timepoint [color=blue, height=0.5, @@ -175,9 +171,8 @@ digraph { width=1.5346]; association -> timepoint [color=blue, label=timepoint, - lp="2480.3,221.5", - pos="e,2468.9,195.21 1440.2,252.07 1449.5,250.01 1459.2,248.16 1468.3,247 1572.8,233.83 2315.4,262.07 2415.3,229 2432.2,223.42 2448.5,\ -212.23 2461.1,201.85", + lp="2486.3,221.5", + pos="e,2465.1,194.83 2447.6,246.69 2446.8,236.76 2447.1,224.26 2451.3,214 2453,209.95 2455.4,206.11 2458.2,202.56", style=solid]; "original subject" [color=blue, height=0.5, @@ -186,49 +181,169 @@ digraph { width=1.0652]; association -> "original subject" [color=blue, label="original subject", - lp="2608.3,221.5", - pos="e,2579.9,194.27 1440.2,252.06 1449.5,250 1459.2,248.15 1468.3,247 1584.2,232.5 2407.5,262.8 2519.3,229 2538.5,223.2 2557.5,211.21 \ -2571.9,200.42", + lp="2599.3,221.5", + pos="e,2575.9,193.16 2482.2,249.32 2494.6,243.35 2508.8,236.17 2521.3,229 2522.6,228.29 2546.6,212.48 2567.3,198.82", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2712.3,178", + pos="2711.3,178", width=1.5887]; association -> "original predicate" [color=blue, label="original predicate", - lp="2752.8,221.5", - pos="e,2702.8,195.82 1440.2,252.04 1449.5,249.98 1459.2,248.14 1468.3,247 1534.5,238.79 2607.8,256.92 2668.3,229 2679.9,223.68 2689.6,\ -213.72 2697,204.09", + lp="2742.8,221.5", + pos="e,2697.8,195.8 2495.9,252.53 2504.7,250.53 2513.8,248.59 2522.3,247 2581.4,236.08 2601.9,254.36 2656.3,229 2669.3,222.98 2681.3,\ +212.85 2690.8,203.27", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2862.3,178", + pos="2825.3,178", width=1.0652]; association -> "original object" [color=blue, label="original object", - lp="2891.8,221.5", - pos="e,2853.4,195.81 1440.2,252.03 1449.5,249.97 1459.2,248.13 1468.3,247 1542.9,237.81 2752.5,261.18 2820.3,229 2831.5,223.72 2840.7,\ -213.91 2847.7,204.36", + lp="2869.8,221.5", + pos="e,2823.5,196.23 2494.7,252.3 2503.8,250.25 2513.3,248.34 2522.3,247 2553.6,242.35 2780.9,247.77 2806.3,229 2813.8,223.53 2818.3,\ +214.8 2821,206.14", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2958.3,178", + width=2.1304]; + association -> "subject category" [color=blue, + label="subject category", + lp="3000.8,221.5", + pos="e,2952,196.07 2494.7,252.17 2503.8,250.12 2513.3,248.26 2522.3,247 2566.7,240.82 2886.4,251.12 2925.3,229 2934.8,223.61 2942.1,214.23 \ +2947.4,205.04", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3129.3,178", + width=2.1304]; + association -> "object category" [color=blue, + label="object category", + lp="3147.8,221.5", + pos="e,3113.5,195.85 2494.3,252.17 2503.5,250.1 2513.2,248.22 2522.3,247 2582.1,239.04 3007.6,249.35 3064.3,229 3079.8,223.45 3094.5,\ +212.75 3106.1,202.67", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3262.3,178", + width=1.0652]; + association -> "subject closure" [color=blue, + label="subject closure", + lp="3285.8,221.5", + pos="e,3249.9,195.36 2494.3,252.12 2503.5,250.06 2513.2,248.19 2522.3,247 2597.9,237.2 3136.7,257.39 3207.3,229 3221.1,223.48 3233.6,\ +212.86 3243.1,202.83", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3360.3,178", + width=1.0652]; + association -> "object closure" [color=blue, + label="object closure", + lp="3402.3,221.5", + pos="e,3358.3,196.39 2494.2,252.09 2503.5,250.03 2513.2,248.17 2522.3,247 2567.4,241.25 3303,254.9 3340.3,229 3348.1,223.66 3352.8,214.83 \ +3355.7,206.07", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3493.3,178", + width=2.1304]; + association -> "subject category closure" [color=blue, + label="subject category closure", + lp="3560.8,221.5", + pos="e,3485.7,196.22 2494.2,252.07 2503.5,250.01 2513.2,248.16 2522.3,247 2573.8,240.5 3410.2,252.8 3456.3,229 3466.5,223.75 3474.6,214.26 \ +3480.6,204.95", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3683.3,178", + width=2.1304]; + association -> "object category closure" [color=blue, + label="object category closure", + lp="3750.8,221.5", + pos="e,3677.7,196.15 2494.2,252.05 2503.5,249.99 2513.2,248.14 2522.3,247 2584.7,239.24 3597.7,259.97 3652.3,229 3661.6,223.76 3668.4,\ +214.54 3673.3,205.43", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3873.3,178", + width=1.0652]; + association -> "subject namespace" [color=blue, + label="subject namespace", + lp="3923.3,221.5", + pos="e,3866.6,195.73 2494.2,252.03 2503.5,249.97 2513.2,248.13 2522.3,247 2558.6,242.52 3806,246.1 3838.3,229 3848.4,223.67 3856.2,213.98 \ +3861.9,204.55", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4032.3,178", + width=1.0652]; + association -> "object namespace" [color=blue, + label="object namespace", + lp="4076.3,221.5", + pos="e,4025,195.76 2494.2,252.02 2503.5,249.96 2513.2,248.13 2522.3,247 2563,242.02 3958.9,247.64 3995.3,229 4005.7,223.71 4013.9,214.03 \ +4019.9,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4183.3,178", + width=1.0652]; + association -> "subject label closure" [color=blue, + label="subject label closure", + lp="4236.3,221.5", + pos="e,4175.4,195.79 2494.2,252.01 2503.5,249.96 2513.2,248.12 2522.3,247 2567.1,241.54 4104,248.99 4144.3,229 4155.1,223.69 4163.7,213.87 \ +4170.1,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4354.3,178", + width=1.0652]; + association -> "object label closure" [color=blue, + label="object label closure", + lp="4402.8,221.5", + pos="e,4346.1,195.8 2493.9,252.09 2503.2,250 2513,248.13 2522.3,247 2571.8,240.99 4269.6,250.79 4314.3,229 4325.2,223.71 4334.1,213.9 \ +4340.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4516.3,178", + width=2.347]; + association -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4564.8,221.5", + pos="e,4507.8,196.3 2493.9,252.09 2503.2,249.99 2513,248.13 2522.3,247 2576.2,240.47 4427.5,252.74 4476.3,229 4487.1,223.79 4495.8,214.18 \ +4502.4,204.76", style=solid]; type [height=0.5, - pos="2988.3,178", + pos="4678.3,178", width=0.86659]; association -> type [color=blue, label=type, - lp="2983.3,221.5", - pos="e,2979.7,195.81 1440.2,252.02 1449.5,249.96 1459.2,248.13 1468.3,247 1509.1,242 2910.3,246.8 2947.3,229 2958.3,223.71 2967.4,213.9 \ -2974.2,204.36", + lp="4673.3,221.5", + pos="e,4670.1,195.81 2493.9,252.08 2503.2,249.99 2513,248.12 2522.3,247 2580.7,239.95 4585.5,254.69 4638.3,229 4649.2,223.72 4658.1,213.9 \ +4664.7,204.36", style=solid]; category [height=0.5, - pos="3089.3,178", + pos="4779.3,178", width=1.4263]; association -> category [color=blue, label=category, - lp="3069.8,221.5", - pos="e,3069.2,194.8 1440.2,252.02 1449.5,249.96 1459.2,248.12 1468.3,247 1553,236.64 2921.1,251.68 3003.3,229 3024,223.3 3044.8,211.39 \ -3060.8,200.62", + lp="4759.8,221.5", + pos="e,4759.2,194.83 2493.9,252.08 2503.2,249.99 2513,248.12 2522.3,247 2642.1,232.55 4577,260.88 4693.3,229 4714,223.34 4734.8,211.43 \ +4750.8,200.65", style=solid]; subject -> object [label=relation, lp="871.35,134.5", @@ -243,11 +358,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="1515.3,265", + pos="2569.3,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1646.3,265", + pos="2700.3,265", width=2.0762]; } diff --git a/graphviz/association.svg b/graphviz/association.svg index e7f2dd8b8c..a9152ecd21 100644 --- a/graphviz/association.svg +++ b/graphviz/association.svg @@ -4,16 +4,16 @@ - + %3 - + association - -association + +association @@ -24,9 +24,9 @@ association->entity - - -is_a + + +is_a @@ -37,9 +37,9 @@ association->id - - -id + + +id @@ -50,9 +50,9 @@ association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ association->name - - -name + + +name @@ -76,9 +76,9 @@ association->description - - -description + + +description @@ -89,9 +89,9 @@ association->has attribute - - -has attribute + + +has attribute @@ -102,8 +102,8 @@ association->subject - - + + subject @@ -115,8 +115,8 @@ association->predicate - - + + predicate @@ -128,7 +128,7 @@ association->object - + object @@ -141,9 +141,9 @@ association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ association->timepoint - - -timepoint + + +timepoint @@ -245,98 +245,241 @@ association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie association->original predicate - - -original predicate + + +original predicate original object - -string + +string association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +association->subject category + + +subject category + + + +object category + +ontology class + + + +association->object category + + +object category + + + +subject closure + +string + + + +association->subject closure + + +subject closure + + + +object closure + +string + + + +association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +association->object category closure + + +object category closure + + + +subject namespace + +string + + + +association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +association->object namespace + + +object namespace + + + +subject label closure + +string + + + +association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + association->type - - -type + + +type - + category - -category + +category - + association->category - - -category + + +category - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/behavior_to_behavioral_feature_association.gv b/graphviz/behavior_to_behavioral_feature_association.gv index c8d6e44258..524771e1e0 100644 --- a/graphviz/behavior_to_behavioral_feature_association.gv +++ b/graphviz/behavior_to_behavioral_feature_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,4596.4,283"]; + graph [bb="0,0,6284.4,283"]; node [label="\N"]; "behavior to behavioral feature association" [height=0.5, label="behavior to behavioral feature association", - pos="2760.4,265", + pos="3444.4,265", width=5.7231]; association [height=0.5, pos="62.394,178", width=1.7332]; "behavior to behavioral feature association" -> association [label=is_a, - lp="582.39,221.5", - pos="e,107.12,190.7 2554,264.82 2165.3,265.46 1297.9,262.53 568.39,229 375.15,220.12 325.55,225.65 134.39,196 128.7,195.12 122.8,194.02 \ -116.92,192.82"]; + lp="572.39,221.5", + pos="e,107.12,190.69 3239.1,263.26 2670.2,260.94 1080.9,252.47 558.39,229 369.57,220.52 321.15,225.14 134.39,196 128.7,195.11 122.8,194.01 \ +116.93,192.81"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "behavior to behavioral feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="745.89,221.5", - pos="e,457.45,194.5 2554.8,263.59 2111.8,262.2 1079.1,256.07 729.39,229 640.44,222.11 539.97,207.7 467.48,196.12"]; + pos="e,457.07,194.55 3238,264.66 2691.7,265.89 1216.1,265.6 729.39,229 640.27,222.3 539.61,207.83 467.11,196.17"]; id [color=blue, height=0.5, label=string, @@ -26,7 +26,7 @@ digraph { "behavior to behavioral feature association" -> id [color=blue, label=id, lp="865.39,221.5", - pos="e,677.38,190 2556.3,262.35 2099.8,258.36 1023.2,247.15 858.39,229 785.36,220.96 767.2,215.65 696.39,196 693.29,195.14 690.09,194.17 \ + pos="e,677.38,190 3239,263.43 2668.6,261.55 1091.7,254.12 858.39,229 785.34,221.13 767.2,215.65 696.39,196 693.29,195.14 690.09,194.17 \ 686.89,193.16", style=solid]; iri [color=blue, @@ -37,7 +37,7 @@ digraph { "behavior to behavioral feature association" -> iri [color=blue, label=iri, lp="982.39,221.5", - pos="e,782.29,190.23 2554.2,264.36 2151.7,264.34 1274.7,260.52 974.39,229 896.98,220.87 877.81,215.26 802.39,196 799.02,195.14 795.54,\ + pos="e,782.29,190.23 3239.4,263.16 2687.3,260.6 1196.2,251.67 974.39,229 896.96,221.08 877.81,215.26 802.39,196 799.02,195.14 795.54,\ 194.18 792.05,193.17", style=solid]; name [color=blue, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "behavior to behavioral feature association" -> name [color=blue, label=name, - lp="1094.4,221.5", - pos="e,907.4,191.24 2556.6,262.18 2139.9,258.1 1217.5,247.15 1074.4,229 1019.8,222.07 958.6,206.16 917.21,194.13", + lp="1093.4,221.5", + pos="e,907.19,191.31 3238.8,263.53 2702,261.95 1284.6,255.31 1073.4,229 1019,222.22 958.13,206.28 916.96,194.21", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "behavior to behavioral feature association" -> description [color=blue, label=description, - lp="1222.9,221.5", - pos="e,1056.1,193.74 2556,262.58 2159.7,259.38 1314.2,250.14 1182.4,229 1142.2,222.55 1098.1,208.71 1065.8,197.22", + lp="1220.9,221.5", + pos="e,1055.3,193.7 3238.1,264.15 2718,264.04 1379.9,260.66 1180.4,229 1140.5,222.66 1096.8,208.74 1064.8,197.19", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "behavior to behavioral feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1380.4,221.5", - pos="e,1197.3,191.84 2557.3,261.96 2191.9,257.85 1450.7,247.36 1333.4,229 1289.4,222.11 1240.8,207.04 1206.9,195.23", + lp="1377.4,221.5", + pos="e,1196.7,191.92 3238.8,263.8 2744.2,262.85 1515.1,257.62 1330.4,229 1287.1,222.29 1239.4,207.19 1206.1,195.33", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "behavior to behavioral feature association" -> predicate [color=blue, label=predicate, - lp="1541.4,221.5", - pos="e,1354.8,193.04 2554.7,263.78 2252.6,262.52 1703.3,256.37 1507.4,229 1458.2,222.12 1403.5,207.57 1364.4,195.93", + lp="1536.4,221.5", + pos="e,1353.7,193.17 3239.4,263.06 2775.1,260.55 1670.5,252.18 1502.4,229 1454.5,222.4 1401.5,207.92 1363.5,196.23", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "behavior to behavioral feature association" -> negated [color=blue, label=negated, - lp="1687.4,221.5", - pos="e,1489.3,190.18 2556.9,262.07 2287.3,258.72 1826.2,250.06 1658.4,229 1602.6,221.99 1539.9,205.27 1499,193.09", + lp="1678.4,221.5", + pos="e,1488.4,190.5 3240.3,262.46 2803.2,258.8 1803.3,248.41 1649.4,229 1596.4,222.32 1537.3,205.82 1498.2,193.59", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "behavior to behavioral feature association" -> qualifiers [color=blue, label=qualifiers, - lp="1823.9,221.5", - pos="e,1638.6,192.94 2557.5,261.8 2317.6,258.3 1932.9,249.6 1790.4,229 1741.7,221.96 1687.5,207.52 1648.6,195.96", + lp="1817.9,221.5", + pos="e,1637.2,193.14 3240.2,262.41 2828.2,258.8 1924.7,248.75 1784.4,229 1737,222.33 1684.6,207.86 1646.9,196.19", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "behavior to behavioral feature association" -> publications [color=blue, label=publications, - lp="1967.4,221.5", - pos="e,1789.2,192.57 2558.9,261.18 2351,257.27 2041,248.35 1923.4,229 1880.3,221.91 1832.8,207.45 1798.8,195.9", + lp="1964.4,221.5", + pos="e,1788.5,192.78 3240.3,262.33 2854.9,258.74 2047,248.93 1920.4,229 1878,222.33 1831.3,207.82 1797.9,196.15", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=2.0943]; "behavior to behavioral feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2121.9,221.5", - pos="e,1947.2,193.53 2565.1,259.23 2396.4,254.14 2166,244.64 2075.4,229 2034.7,221.98 1990,208.24 1957.1,196.95", + lp="2124.9,221.5", + pos="e,1947.2,193.58 3241.7,261.72 2889.2,257.31 2189.8,246.5 2078.4,229 2036.5,222.42 1990.4,208.42 1956.8,196.9", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -127,8 +127,8 @@ digraph { width=3.015]; "behavior to behavioral feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2272.9,221.5", - pos="e,2135.8,195.65 2562.7,259.89 2431.9,255.56 2273.2,246.75 2208.4,229 2186.1,222.89 2163,211.4 2144.8,200.97", + lp="2282.9,221.5", + pos="e,2137.7,195.42 3239.8,262.66 2916.7,259.85 2314.6,251.64 2218.4,229 2193.3,223.09 2167,211.05 2146.6,200.26", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -137,8 +137,8 @@ digraph { width=3.015]; "behavior to behavioral feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2442.4,221.5", - pos="e,2340.9,196.03 2566.1,258.99 2466.8,254.41 2363.3,245.66 2347.4,229 2341.7,223 2339.9,214.5 2340,206.21", + lp="2456.4,221.5", + pos="e,2346.1,196.25 3239.1,263.41 2934.8,261.68 2395.7,254.94 2361.4,229 2354.2,223.55 2350.2,214.82 2347.9,206.17", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -147,8 +147,8 @@ digraph { width=3.015]; "behavior to behavioral feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2650.9,221.5", - pos="e,2556.3,195.72 2606,253.08 2577.6,247.89 2554,240.25 2544.4,229 2537.4,220.81 2541.5,211.34 2549,202.86", + lp="2665.9,221.5", + pos="e,2564.7,196.05 3239.5,262.97 2985.4,260.66 2582.6,253.18 2559.4,229 2552.9,222.25 2554.6,213.2 2559.2,204.65", style=solid]; timepoint [color=blue, height=0.5, @@ -157,8 +157,8 @@ digraph { width=1.5346]; "behavior to behavioral feature association" -> timepoint [color=blue, label=timepoint, - lp="2796.4,221.5", - pos="e,2761.9,196.09 2760.7,246.87 2760.9,237.22 2761.1,224.94 2761.4,214 2761.5,211.45 2761.5,208.79 2761.6,206.13", + lp="2824.4,221.5", + pos="e,2766.8,195.94 3239.4,263.02 3061.6,260.55 2826.9,252.74 2789.4,229 2780.8,223.57 2774.8,214.44 2770.6,205.45", style=solid]; "original subject" [color=blue, height=0.5, @@ -167,8 +167,8 @@ digraph { width=1.0652]; "behavior to behavioral feature association" -> "original subject" [color=blue, label="original subject", - lp="2903.4,221.5", - pos="e,2863,195.37 2801.5,247.22 2811.7,242.12 2822.4,235.99 2831.4,229 2840.7,221.77 2849.5,212.26 2856.7,203.47", + lp="2924.4,221.5", + pos="e,2866.3,195.95 3252,258.54 3089.7,252.97 2881.7,243.12 2868.4,229 2862.6,222.84 2862,214.21 2863.6,205.84", style=solid]; "original predicate" [color=blue, height=0.5, @@ -177,8 +177,8 @@ digraph { width=1.5887]; "behavior to behavioral feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3039.9,221.5", - pos="e,2984.2,195.99 2890,250.95 2921.9,245.69 2950.5,238.54 2963.4,229 2971.2,223.2 2976.7,214.27 2980.6,205.56", + lp="3053.9,221.5", + pos="e,2983.9,196.05 3244.3,260.67 3131.1,256.68 3008.7,247.98 2990.4,229 2984.6,223.02 2982.9,214.53 2983,206.24", style=solid]; "original object" [color=blue, height=0.5, @@ -187,161 +187,277 @@ digraph { width=1.0652]; "behavior to behavioral feature association" -> "original object" [color=blue, label="original object", - lp="3164.9,221.5", - pos="e,3109.9,195.86 2901.9,251.86 2996.3,243.43 3103.8,233.01 3107.4,229 3113.1,222.74 3113.7,214.08 3112.4,205.72", + lp="3187.9,221.5", + pos="e,3109.3,195.81 3264.7,256.2 3210.4,251.13 3159.2,242.77 3136.4,229 3127,223.3 3119.5,213.87 3114.1,204.72", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3235.4,178", + width=2.1304]; + "behavior to behavioral feature association" -> "subject category" [color=blue, + label="subject category", + lp="3312.9,221.5", + pos="e,3237.2,196.31 3318.7,250.69 3289.9,245.48 3264.5,238.43 3253.4,229 3246.6,223.23 3242.4,214.69 3239.7,206.29", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3406.4,178", + width=2.1304]; + "behavior to behavioral feature association" -> "object category" [color=blue, + label="object category", + lp="3433.9,221.5", + pos="e,3387.5,195.82 3397.2,247.32 3389.7,242.57 3382.9,236.56 3378.4,229 3373.5,220.9 3376.1,211.93 3381.3,203.84", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3539.4,178", + width=1.0652]; + "behavior to behavioral feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="3559.9,221.5", + pos="e,3524.6,194.83 3467.3,247.09 3474.5,241.51 3482.4,235.16 3489.4,229 3498.9,220.58 3508.9,210.78 3517.5,202.1", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3639.4,178", + width=1.0652]; + "behavior to behavioral feature association" -> "object closure" [color=blue, + label="object closure", + lp="3680.4,221.5", + pos="e,3636.4,196.31 3556.4,249.84 3583.5,244.56 3607.8,237.68 3618.4,229 3625.5,223.17 3630.3,214.5 3633.4,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3772.4,178", + width=2.1304]; + "behavior to behavioral feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3838.9,221.5", + pos="e,3763.9,196.31 3585.7,251.88 3652.6,245.24 3720.8,236.8 3734.4,229 3744.3,223.33 3752.4,213.95 3758.6,204.83", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3964.4,178", + width=2.1304]; + "behavior to behavioral feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4029.9,221.5", + pos="e,3957.6,196 3590.1,252.23 3613.3,250.43 3637,248.63 3659.4,247 3689.5,244.81 3904.2,243.99 3930.4,229 3940,223.52 3947.4,214.13 \ +3952.8,204.95", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4154.4,178", + width=1.0652]; + "behavior to behavioral feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4202.4,221.5", + pos="e,4146.7,196.14 3586.6,251.96 3610.9,250.13 3635.8,248.39 3659.4,247 3710.2,243.99 4072.4,252.81 4117.4,229 4127.5,223.64 4135.6,\ +214.14 4141.6,204.85", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4313.4,178", + width=1.0652]; + "behavior to behavioral feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4356.4,221.5", + pos="e,4305.4,195.71 3585.4,251.84 3610.1,250.01 3635.5,248.3 3659.4,247 3693.5,245.15 4243.9,244.44 4274.4,229 4285.1,223.59 4293.7,\ +213.76 4300.1,204.24", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4464.4,178", + width=1.0652]; + "behavior to behavioral feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4516.4,221.5", + pos="e,4456.1,195.75 3584.5,251.79 3609.5,249.94 3635.2,248.24 3659.4,247 3701.9,244.82 4386.3,247.87 4424.4,229 4435.2,223.64 4444.1,\ +213.81 4450.7,204.28", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4603.4,178", + width=1.0652]; + "behavior to behavioral feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="4672.9,221.5", + pos="e,4605.3,196.04 3584,251.75 3609.1,249.89 3635,248.2 3659.4,247 3685.3,245.73 4574.6,245.85 4594.4,229 4601,223.39 4603.8,214.73 \ +4604.9,206.19", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4744.4,178", + width=2.347]; + "behavior to behavioral feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4822.9,221.5", + pos="e,4750.8,196.11 3583.7,251.71 3608.9,249.85 3634.9,248.17 3659.4,247 3689.6,245.56 4725.2,250.53 4746.4,229 4752.3,223.01 4753.4,\ +214.41 4752.6,206.03", style=solid]; type [height=0.5, - pos="3190.4,178", + pos="4878.4,178", width=0.86659]; "behavior to behavioral feature association" -> type [color=blue, label=type, - lp="3240.4,221.5", - pos="e,3208.3,193.2 2906.7,252.32 2929.7,250.52 2953.2,248.69 2975.4,247 3002.6,244.92 3201.8,249 3220.4,229 3228.1,220.66 3223.3,209.99 \ -3215.4,200.65", + lp="4917.4,221.5", + pos="e,4891.4,194.36 3583.4,251.69 3608.7,249.83 3634.8,248.15 3659.4,247 3676.6,246.2 4884.3,241.24 4896.4,229 4903.3,222 4901.3,212.17 \ +4896.7,203.08", style=solid]; category [height=0.5, - pos="3291.4,178", + pos="4979.4,178", width=1.4263]; "behavior to behavioral feature association" -> category [color=blue, label=category, - lp="3306.9,221.5", - pos="e,3285.6,195.97 2905.5,252.21 2928.9,250.4 2952.8,248.61 2975.4,247 3007,244.75 3233.2,245.3 3260.4,229 3269.5,223.55 3276.3,214.29 \ -3281.2,205.2", + lp="4988.9,221.5", + pos="e,4970.5,195.81 3583.4,251.68 3608.7,249.82 3634.8,248.14 3659.4,247 3694.9,245.35 4905.3,244.22 4937.4,229 4948.5,223.72 4957.8,\ +213.9 4964.7,204.36", style=solid]; subject [height=0.5, - pos="3405.4,178", + pos="5093.4,178", width=1.2277]; "behavior to behavioral feature association" -> subject [color=blue, label=subject, - lp="3393.4,221.5", - pos="e,3390.6,195.27 2903.8,252.06 2927.7,250.25 2952.2,248.48 2975.4,247 3056.9,241.78 3266,257.76 3342.4,229 3357.5,223.3 3371.9,212.52 \ -3383,202.42", + lp="5079.4,221.5", + pos="e,5077.5,195 3583.1,251.69 3608.5,249.82 3634.7,248.14 3659.4,247 3735.2,243.51 4952.4,252.87 5024.4,229 5041.2,223.42 5057.4,212.12 \ +5069.9,201.67", style=solid]; object [height=0.5, - pos="3448.4,91", + pos="5136.4,91", width=1.0832]; "behavior to behavioral feature association" -> object [color=blue, label=object, - lp="3491.4,178", - pos="e,3461.8,108.09 2902.9,251.95 2927.1,250.13 2951.9,248.4 2975.4,247 3025.1,244.04 3377.5,248.31 3423.4,229 3464.1,211.88 3466.2,\ -185.85 3471.4,142 3472.2,135.38 3473.3,133.39 3471.4,127 3470.4,123.55 3468.9,120.13 3467.1,116.85", + lp="5179.4,178", + pos="e,5149.8,108.09 3583.1,251.67 3608.5,249.8 3634.7,248.13 3659.4,247 3699.6,245.16 5071.8,243.58 5109.4,229 5151,212.86 5154.1,186.29 \ +5159.4,142 5160.2,135.38 5161.3,133.39 5159.4,127 5158.4,123.55 5156.9,120.13 5155.1,116.85", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3632.4,178", + pos="5320.4,178", width=2.3651]; "behavior to behavioral feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3620.4,221.5", - pos="e,3599.7,194.74 2902,251.9 2926.5,250.07 2951.7,248.35 2975.4,247 3091.7,240.41 3385.1,251.8 3499.4,229 3530.8,222.73 3564.6,209.95 \ -3590.3,198.88", + lp="5308.4,221.5", + pos="e,5288.2,194.71 3583.1,251.66 3608.5,249.79 3634.7,248.12 3659.4,247 3829,239.3 5020.5,260.35 5187.4,229 5219.1,223.04 5253.1,210.12 \ +5278.8,198.91", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="3811.4,178", + pos="5499.4,178", width=2.1123]; "behavior to behavioral feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="3801.4,221.5", - pos="e,3782.6,194.71 2900.8,251.8 2925.7,249.96 2951.3,248.26 2975.4,247 3055,242.86 3614.5,245.72 3692.4,229 3720.7,222.92 3750.7,210.25 \ -3773.6,199.18", + lp="5489.4,221.5", + pos="e,5470.6,194.84 3582.8,251.65 3608.3,249.78 3634.6,248.11 3659.4,247 3754.9,242.73 5286.8,248.38 5380.4,229 5408.7,223.13 5438.8,\ +210.45 5461.6,199.33", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="3941.4,178", + pos="5629.4,178", width=1.011]; "behavior to behavioral feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="3948.9,221.5", - pos="e,3924.7,194.24 2900.3,251.74 2925.3,249.89 2951.1,248.21 2975.4,247 3024.8,244.55 3819.2,243.83 3866.4,229 3884.8,223.22 3902.9,\ -211.39 3916.7,200.7", + lp="5637.9,221.5", + pos="e,5612.7,194.31 3582.8,251.63 3608.3,249.76 3634.6,248.1 3659.4,247 3712,244.67 5504.1,244.49 5554.4,229 5572.8,223.32 5590.9,211.5 \ +5604.7,200.77", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="4069.4,178", + pos="5757.4,178", width=2.0401]; "behavior to behavioral feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="4076.4,221.5", - pos="e,4053.8,195.7 2899.7,251.73 2924.9,249.87 2950.9,248.18 2975.4,247 3032.5,244.25 3950.4,247.88 4004.4,229 4020,223.54 4034.8,212.73 \ -4046.4,202.56", + lp="5765.4,221.5", + pos="e,5742.1,195.74 3582.5,251.64 3608.1,249.76 3634.5,248.09 3659.4,247 3715.8,244.52 5640.1,247.63 5693.4,229 5708.9,223.6 5723.5,\ +212.8 5734.8,202.62", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="4205.4,178", + pos="5893.4,178", width=1.2277]; "behavior to behavioral feature association" -> "has count" [color=blue, label="has count", - lp="4193.4,221.5", - pos="e,4186.8,194.52 2899.7,251.69 2924.9,249.84 2950.9,248.16 2975.4,247 3039.2,243.98 4063.1,246.91 4124.4,229 4144,223.26 4163.6,211.39 \ -4178.6,200.66", + lp="5881.4,221.5", + pos="e,5875.1,194.57 3582.5,251.63 3608.1,249.75 3634.5,248.09 3659.4,247 3719.2,244.39 5755.9,245.74 5813.4,229 5832.8,223.33 5852.2,\ +211.47 5867,200.71", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="4311.4,178", + pos="5999.4,178", width=1.2277]; "behavior to behavioral feature association" -> "has total" [color=blue, label="has total", - lp="4296.9,221.5", - pos="e,4293.4,194.53 2899.4,251.69 2924.7,249.83 2950.8,248.15 2975.4,247 3045.2,243.75 4165.5,248.92 4232.4,229 4251.6,223.27 4270.7,\ -211.4 4285.3,200.67", + lp="5984.9,221.5", + pos="e,5981.4,194.57 3582.5,251.62 3608.1,249.75 3634.5,248.08 3659.4,247 3722.1,244.27 5860.1,246.73 5920.4,229 5939.7,223.33 5958.8,\ +211.47 5973.3,200.71", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="4415.4,178", + pos="6103.4,178", width=1.1735]; "behavior to behavioral feature association" -> "has quotient" [color=blue, label="has quotient", - lp="4411.4,221.5", - pos="e,4396.6,194.3 2899.1,251.69 2924.5,249.82 2950.7,248.14 2975.4,247 3050.7,243.53 4259.9,249.67 4332.4,229 4352.5,223.26 4372.7,\ -211.26 4388.2,200.47", + lp="6099.4,221.5", + pos="e,6084.7,194.34 3582.5,251.62 3608.1,249.74 3634.5,248.08 3659.4,247 3724.9,244.16 5957.3,246.8 6020.4,229 6040.6,223.31 6060.8,\ +211.32 6076.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4522.4,178", + pos="6210.4,178", width=1.1735]; "behavior to behavioral feature association" -> "has percentage" [color=blue, label="has percentage", - lp="4541.4,221.5", - pos="e,4507.9,195.47 2899.1,251.67 2924.5,249.8 2950.7,248.12 2975.4,247 3016.6,245.12 4421.6,242.97 4460.4,229 4475.5,223.58 4489.6,\ -212.82 4500.6,202.67", + lp="6229.4,221.5", + pos="e,6196.4,195 3582.5,251.61 3608.1,249.73 3634.5,248.07 3659.4,247 3728.5,244.02 6083.3,252.25 6148.4,229 6163.7,223.54 6178,212.56 \ +6189,202.28", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3022.4,265", + pos="3706.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3153.4,265", + pos="3837.4,265", width=2.0762]; subject -> object [label=relation, - lp="3443.4,134.5", - pos="e,3430.5,107.23 3406.5,159.55 3407.7,149.57 3410.2,137.07 3415.4,127 3417.6,122.68 3420.5,118.52 3423.7,114.66"]; + lp="5131.4,134.5", + pos="e,5118.5,107.23 5094.5,159.55 5095.7,149.57 5098.2,137.07 5103.4,127 5105.6,122.68 5108.5,118.52 5111.7,114.66"]; relation [height=0.5, - pos="3393.4,18", + pos="5081.4,18", width=1.2999]; - subject -> relation [pos="e,3394.7,36.188 3404.1,159.79 3402,132.48 3398,78.994 3395.5,46.38", + subject -> relation [pos="e,5082.7,36.188 5092.1,159.79 5090,132.48 5086,78.994 5083.5,46.38", style=dotted]; "behavior to behavioral feature association_subject" [color=blue, height=0.5, label=behavior, - pos="3297.4,265", + pos="3981.4,265", width=1.4263]; - object -> relation [pos="e,3406.2,35.54 3435.9,73.889 3429,64.939 3420.2,53.617 3412.4,43.584", + object -> relation [pos="e,5094.2,35.54 5123.9,73.889 5117,64.939 5108.2,53.617 5100.4,43.584", style=dotted]; "behavior to behavioral feature association_object" [color=blue, height=0.5, label="behavioral feature", - pos="3463.4,265", + pos="4147.4,265", width=2.672]; } diff --git a/graphviz/behavior_to_behavioral_feature_association.svg b/graphviz/behavior_to_behavioral_feature_association.svg index 510c35cfd0..7bb9c0d068 100644 --- a/graphviz/behavior_to_behavioral_feature_association.svg +++ b/graphviz/behavior_to_behavioral_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + behavior to behavioral feature association - -behavior to behavioral feature association + +behavior to behavioral feature association @@ -24,9 +24,9 @@ behavior to behavioral feature association->association - - -is_a + + +is_a @@ -37,8 +37,8 @@ behavior to behavioral feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,7 +50,7 @@ behavior to behavioral feature association->id - + id @@ -63,7 +63,7 @@ behavior to behavioral feature association->iri - + iri @@ -76,9 +76,9 @@ behavior to behavioral feature association->name - - -name + + +name @@ -89,9 +89,9 @@ behavior to behavioral feature association->description - - -description + + +description @@ -102,9 +102,9 @@ behavior to behavioral feature association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ behavior to behavioral feature association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ behavior to behavioral feature association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ behavior to behavioral feature association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ behavior to behavioral feature association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ behavior to behavioral feature association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ behavior to behavioral feature association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ behavior to behavioral feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ behavior to behavioral feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ behavior to behavioral feature association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ behavior to behavioral feature association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ behavior to behavioral feature association->original predicate - - -original predicate + + +original predicate @@ -258,214 +258,357 @@ behavior to behavioral feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +behavior to behavioral feature association->subject category + + +subject category + + + +object category + +ontology class + + + +behavior to behavioral feature association->object category + + +object category + + + +subject closure + +string + + + +behavior to behavioral feature association->subject closure + + +subject closure + + + +object closure + +string + + + +behavior to behavioral feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +behavior to behavioral feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +behavior to behavioral feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +behavior to behavioral feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +behavior to behavioral feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +behavior to behavioral feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +behavior to behavioral feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +behavior to behavioral feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + behavior to behavioral feature association->type - - -type + + +type - + category - -category + +category - + behavior to behavioral feature association->category - - -category + + +category - + subject - -subject + +subject - + behavior to behavioral feature association->subject - - -subject + + +subject - + object - -object + +object - + behavior to behavioral feature association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + behavior to behavioral feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + behavior to behavioral feature association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + behavior to behavioral feature association->onset qualifier - - -onset qualifier + + +onset qualifier - + sex qualifier - -biological sex + +biological sex - + behavior to behavioral feature association->sex qualifier - - -sex qualifier + + +sex qualifier - + has count - -integer + +integer - + behavior to behavioral feature association->has count - - -has count + + +has count - + has total - -integer + +integer - + behavior to behavioral feature association->has total - - -has total + + +has total - + has quotient - -double + +double - + behavior to behavioral feature association->has quotient - - -has quotient + + +has quotient - + has percentage - -double + +double - + behavior to behavioral feature association->has percentage - - -has percentage + + +has percentage - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + behavior to behavioral feature association_subject - -behavior + +behavior - + object->relation - - + + - + behavior to behavioral feature association_object - -behavioral feature + +behavioral feature diff --git a/graphviz/case_to_phenotypic_feature_association.gv b/graphviz/case_to_phenotypic_feature_association.gv index 19287d016d..6c1f59bc54 100644 --- a/graphviz/case_to_phenotypic_feature_association.gv +++ b/graphviz/case_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4981.4,283"]; + graph [bb="0,0,6661.4,283"]; node [label="\N"]; "case to phenotypic feature association" [height=0.5, label="case to phenotypic feature association", - pos="2763.4,265", + pos="3673.4,265", width=5.2356]; association [height=0.5, pos="62.394,178", width=1.7332]; "case to phenotypic feature association" -> association [label=is_a, - lp="704.39,221.5", - pos="e,106.72,190.73 2575.4,263.49 2211.4,261.92 1385,255.47 690.39,229 443.03,219.58 379.32,231.91 134.39,196 128.61,195.15 122.62,194.07 \ + lp="699.39,221.5", + pos="e,106.72,190.73 3485.9,262.99 2920,259.74 1234.4,248.64 685.39,229 440.22,220.23 377.12,231.65 134.39,196 128.61,195.15 122.62,194.07 \ 116.66,192.86"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "case to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, - lp="935.89,221.5", - pos="e,492.99,192.95 2574.8,264.86 2240.8,265.38 1523.7,262.06 919.39,229 777.05,221.21 614.58,205.69 502.96,194"]; + lp="927.89,221.5", + pos="e,490.35,193.09 3485.2,263.55 2947.9,261.97 1413.8,255.23 911.39,229 770.87,221.66 610.5,206.04 500.5,194.19"]; "case to entity association mixin" [height=0.5, pos="767.39,178", width=4.3691]; "case to phenotypic feature association" -> "case to entity association mixin" [label=uses, lp="1077.9,221.5", - pos="e,838.29,194.09 2575.3,263.64 2195.9,262.34 1350,256.36 1061.4,229 988.79,222.12 907.08,207.67 848.27,196.07"]; + pos="e,837.68,194.11 3485.7,263.17 2927.3,260.46 1300.2,250.77 1061.4,229 988.53,222.36 906.51,207.81 847.66,196.11"]; id [color=blue, height=0.5, label=string, @@ -32,8 +32,8 @@ digraph { "case to phenotypic feature association" -> id [color=blue, label=id, lp="1196.4,221.5", - pos="e,1010.4,189.98 2575.1,264.08 2217.5,263.54 1452.2,258.78 1189.4,229 1117.2,220.83 1099.3,215.5 1029.4,196 1026.3,195.13 1023.1,\ -194.17 1019.9,193.15", + pos="e,1010.4,189.98 3485.3,263.4 2945.4,261.4 1414.8,253.6 1189.4,229 1117.2,221.12 1099.3,215.5 1029.4,196 1026.3,195.13 1023.1,194.17 \ +1019.9,193.15", style=solid]; iri [color=blue, height=0.5, @@ -43,7 +43,7 @@ digraph { "case to phenotypic feature association" -> iri [color=blue, label=iri, lp="1303.4,221.5", - pos="e,1115.3,190.16 2575.3,263.72 2236.8,262.51 1537.5,256.63 1295.4,229 1223.3,220.77 1205.6,214.45 1135.4,196 1132,195.11 1128.5,194.14 \ + pos="e,1115.3,190.16 3485.5,263.27 2961.7,260.97 1510,252.5 1295.4,229 1223.2,221.1 1205.6,214.45 1135.4,196 1132,195.11 1128.5,194.14 \ 1125.1,193.12", style=solid]; name [color=blue, @@ -54,7 +54,7 @@ digraph { "case to phenotypic feature association" -> name [color=blue, label=name, lp="1407.4,221.5", - pos="e,1238.3,191.69 2574.6,264.72 2252.7,265.03 1610.6,261.37 1387.4,229 1338.9,221.97 1285.1,206.63 1247.8,194.78", + pos="e,1238.2,191.81 3484.9,263.79 2974.8,262.83 1591.9,257.61 1387.4,229 1338.9,222.22 1285,206.84 1247.8,194.91", style=solid]; description [color=blue, height=0.5, @@ -64,7 +64,7 @@ digraph { "case to phenotypic feature association" -> description [color=blue, label=description, lp="1523.9,221.5", - pos="e,1383.1,194.44 2576.9,262.34 2247.5,258.89 1587.4,249.52 1483.4,229 1451.8,222.78 1418,209.8 1392.4,198.62", + pos="e,1382.8,194.43 3486.2,262.76 2973.9,259.14 1580.8,247.63 1483.4,229 1451.7,222.94 1417.7,209.88 1392.1,198.63", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +74,7 @@ digraph { "case to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1662.4,221.5", - pos="e,1523.3,193.71 2577.4,262.05 2276.3,258.34 1706.4,248.79 1615.4,229 1586.3,222.68 1555.4,209.48 1532.4,198.22", + pos="e,1522.9,193.58 3486,262.74 2995.6,259.17 1705.9,248.04 1615.4,229 1586.1,222.84 1555,209.49 1531.9,198.13", style=solid]; subject [color=blue, height=0.5, @@ -84,7 +84,7 @@ digraph { "case to phenotypic feature association" -> subject [color=blue, label=subject, lp="1789.4,221.5", - pos="e,1666.5,194.26 2579.6,260.94 2312.6,255.97 1840.7,245.08 1763.4,229 1733,222.68 1700.4,209.72 1675.9,198.58", + pos="e,1666.3,194.29 3485,264.35 3036.2,264.64 1928.7,261.94 1763.4,229 1732.8,222.91 1700.1,209.88 1675.6,198.64", style=solid]; predicate [color=blue, height=0.5, @@ -94,7 +94,7 @@ digraph { "case to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1868.4,221.5", - pos="e,1808.4,196.08 2578.5,261.41 2316.7,257.11 1866.1,247.12 1834.4,229 1825,223.63 1817.9,214.25 1812.9,205.06", + pos="e,1808.4,196.15 3486.1,262.75 3025.1,259.38 1870.1,248.96 1834.4,229 1825,223.71 1817.9,214.35 1812.8,205.15", style=solid]; object [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { "case to phenotypic feature association" -> object [color=blue, label=object, lp="1947.4,178", - pos="e,1776,105.47 2594,257.09 2366.4,246.75 1983.4,225.31 1925.4,196 1905.2,185.8 1908.1,172.77 1889.4,160 1857.3,138.07 1817,120.64 \ -1785.5,108.92", + pos="e,1776,105.47 3486.2,262.74 3136.6,259.88 2396.9,251.34 2141.4,229 2044.6,220.54 2012,239.85 1925.4,196 1905.2,185.78 1908.1,172.77 \ +1889.4,160 1857.3,138.07 1817,120.64 1785.5,108.92", style=solid]; negated [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=1.2999]; "case to phenotypic feature association" -> negated [color=blue, label=negated, - lp="2245.4,221.5", - pos="e,2059.8,190.35 2581.5,260.29 2474.6,256.14 2337.3,247.39 2216.4,229 2165.2,221.22 2108,205.22 2069.6,193.4", + lp="2250.4,221.5", + pos="e,2059.6,190.46 3485,264.27 3149.2,263.96 2460,259.46 2221.4,229 2168.1,222.19 2108.5,205.66 2069.1,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=2.1304]; "case to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2373.9,221.5", - pos="e,2207.3,193.25 2591.8,257.5 2514.5,252.6 2422.4,244.02 2340.4,229 2298.2,221.27 2251.5,207.56 2217.1,196.45", + lp="2389.9,221.5", + pos="e,2208.5,193.07 3485,264.34 3174.5,263.99 2568.3,259.29 2356.4,229 2308.8,222.2 2256.1,207.74 2218.2,196.11", style=solid]; publications [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=1.7332]; "case to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2505.4,221.5", - pos="e,2356.2,193.34 2615.5,253.78 2566.1,248.53 2511,240.69 2461.4,229 2428.5,221.24 2392.6,208.09 2365.7,197.22", + lp="2537.4,221.5", + pos="e,2359.9,192.71 3484.9,264.28 3201.3,263.69 2678.5,258.46 2493.4,229 2450.5,222.18 2403.3,207.69 2369.5,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -144,8 +144,8 @@ digraph { width=2.0943]; "case to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2636.9,221.5", - pos="e,2509.3,194.68 2670.8,249.24 2644.5,243.98 2616.1,237.26 2590.4,229 2565.8,221.08 2539.4,209.32 2518.5,199.19", + lp="2691.9,221.5", + pos="e,2517.6,193.61 3485.5,263.4 3234,261.6 2801.5,254.72 2645.4,229 2604.8,222.3 2560.1,208.48 2527.4,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -154,8 +154,8 @@ digraph { width=3.015]; "case to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2759.9,221.5", - pos="e,2682.8,196.34 2718.2,247.43 2709.7,242.58 2701.5,236.51 2695.4,229 2690.1,222.52 2686.8,214.16 2684.8,206.15", + lp="2846.9,221.5", + pos="e,2707.2,195.59 3489.7,260.88 3248.7,256.16 2848.7,245.9 2782.4,229 2759.1,223.06 2734.9,211.3 2716,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -164,9 +164,8 @@ digraph { width=3.015]; "case to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2942.4,221.5", - pos="e,2882.7,195.19 2793.7,247.07 2803.6,241.44 2814.5,235.06 2824.4,229 2834.8,222.63 2836.8,220.1 2847.4,214 2855.8,209.16 2864.9,\ -204.28 2873.7,199.76", + lp="3018.4,221.5", + pos="e,2913.8,196.37 3488.9,261.23 3273.6,257.14 2944,247.82 2923.4,229 2917.2,223.35 2914.7,214.95 2913.9,206.63", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -175,9 +174,8 @@ digraph { width=3.015]; "case to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3166.9,221.5", - pos="e,3105.7,194.43 2898.4,252.43 2954.1,246.48 3011.6,238.48 3037.4,229 3048.8,224.79 3049.5,219.55 3060.4,214 3071.7,208.22 3084.2,\ -202.83 3096.2,198.09", + lp="3226.9,221.5", + pos="e,3130.1,195.91 3484.7,264.54 3334.4,262.95 3145.3,255.56 3120.4,229 3113.3,221.47 3116.7,212.1 3123.3,203.51", style=solid]; timepoint [color=blue, height=0.5, @@ -186,9 +184,8 @@ digraph { width=1.5346]; "case to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3330.4,221.5", - pos="e,3316.5,195.18 2895.4,252.15 2917.4,250.32 2940.1,248.53 2961.4,247 3030.7,242.03 3208.8,254.51 3273.4,229 3281.3,225.86 3296,213.72 \ -3308.8,202.19", + lp="3381.4,221.5", + pos="e,3333.2,196.41 3515.7,255.11 3438.8,249.34 3360,240.7 3346.4,229 3339.8,223.34 3336.4,214.82 3334.6,206.41", style=solid]; "original subject" [color=blue, height=0.5, @@ -197,9 +194,8 @@ digraph { width=1.0652]; "case to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3445.4,221.5", - pos="e,3423.3,192.7 2894.1,252.01 2916.5,250.17 2939.6,248.42 2961.4,247 3051.3,241.15 3280.6,256.58 3366.4,229 3378,225.26 3379.1,220.57 \ -3389.4,214 3397.6,208.79 3406.4,203.21 3414.7,198.07", + lp="3479.4,221.5", + pos="e,3430.2,194.78 3504.8,256.92 3467.7,251.73 3435.7,243.14 3423.4,229 3417,221.59 3419.3,212 3424.4,203.21", style=solid]; "original predicate" [color=blue, height=0.5, @@ -208,9 +204,8 @@ digraph { width=1.5887]; "case to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3586.9,221.5", - pos="e,3542.8,195.49 2893,251.89 2915.8,250.04 2939.3,248.32 2961.4,247 3021.3,243.43 3445.5,250.84 3501.4,229 3509.1,225.98 3523.2,213.98 \ -3535.5,202.49", + lp="3605.9,221.5", + pos="e,3546.4,195.6 3585.7,249 3565.8,243.77 3548.6,237.12 3542.4,229 3537,221.92 3538.1,212.99 3541.6,204.65", style=solid]; "original object" [color=blue, height=0.5, @@ -219,115 +214,232 @@ digraph { width=1.0652]; "case to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3715.9,221.5", - pos="e,3670.6,196.43 2892.2,251.82 2915.2,249.96 2939,248.25 2961.4,247 2999.7,244.86 3619.6,250.37 3651.4,229 3659.3,223.7 3664.4,214.88 \ -3667.6,206.11", + lp="3724.9,221.5", + pos="e,3673.4,196.18 3673.4,246.8 3673.4,235.16 3673.4,219.55 3673.4,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3806.4,178", + width=2.1304]; + "case to phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3849.9,221.5", + pos="e,3800.2,195.97 3743.3,248.25 3755.5,243.41 3767.4,237.13 3777.4,229 3785.2,222.66 3791.3,213.66 3795.9,205.03", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3977.4,178", + width=2.1304]; + "case to phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3993.9,221.5", + pos="e,3961.1,195.71 3824.2,254.16 3854.6,248.85 3885.6,240.88 3913.4,229 3928,222.76 3942.1,212.32 3953.4,202.6", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4110.4,178", + width=1.0652]; + "case to phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="4127.9,221.5", + pos="e,4094.9,194.58 3806.5,252.22 3914.9,242.55 4050.5,230.25 4053.4,229 4061.1,225.69 4075.3,213.26 4087.6,201.63", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4206.4,178", + width=1.0652]; + "case to phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4247.4,221.5", + pos="e,4203.9,196.3 3805.4,252.14 3827.4,250.31 3850.1,248.53 3871.4,247 3906.3,244.51 4156.9,249.17 4185.4,229 4193.1,223.55 4198,214.7 \ +4201.1,205.95", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4339.4,178", + width=2.1304]; + "case to phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4405.9,221.5", + pos="e,4331.4,196.14 3803.8,251.99 3826.3,250.14 3849.5,248.4 3871.4,247 3919.1,243.95 4259,251.14 4301.4,229 4311.6,223.64 4319.9,214.14 \ +4326.1,204.85", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4528.4,178", + width=2.1304]; + "case to phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4595.9,221.5", + pos="e,4522.7,196.1 3802.5,251.85 3825.4,250 3849.1,248.28 3871.4,247 3906.1,245.01 4467.2,246.36 4497.4,229 4506.6,223.71 4513.4,214.47 \ +4518.3,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4718.4,178", + width=1.0652]; + "case to phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4768.4,221.5", + pos="e,4711.4,196.19 3801.7,251.79 3824.8,249.93 3848.8,248.22 3871.4,247 3916.5,244.57 4643.6,250.28 4683.4,229 4693.2,223.75 4700.9,\ +214.4 4706.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4877.4,178", + width=1.0652]; + "case to phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4921.4,221.5", + pos="e,4870,195.73 3801.4,251.75 3824.7,249.88 3848.7,248.18 3871.4,247 3925.2,244.2 4792.5,253.68 4840.4,229 4850.7,223.67 4858.9,213.99 \ +4864.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="5028.4,178", + width=1.0652]; + "case to phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5081.4,221.5", + pos="e,5020.4,195.77 3801.1,251.72 3824.5,249.85 3848.7,248.16 3871.4,247 3902.4,245.42 4961.6,242.85 4989.4,229 5000.1,223.66 5008.8,\ +213.84 5015.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5166.4,178", + width=1.0652]; + "case to phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5237.9,221.5", + pos="e,5169.1,195.98 3800.9,251.7 3824.3,249.83 3848.6,248.14 3871.4,247 3907.1,245.22 5132.6,252.67 5159.4,229 5165.8,223.31 5168.4,\ +214.64 5169.1,206.11", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5307.4,178", + width=2.347]; + "case to phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5386.9,221.5", + pos="e,5314.7,196.1 3800.6,251.7 3824.1,249.81 3848.5,248.13 3871.4,247 3891.4,246.02 5297.3,243.23 5311.4,229 5317.3,223.01 5318.2,214.41 \ +5317,206.03", style=solid]; type [height=0.5, - pos="3761.4,178", + pos="5441.4,178", width=0.86659]; "case to phenotypic feature association" -> type [color=blue, label=type, - lp="3793.4,221.5", - pos="e,3771.3,195.51 2891.7,251.79 2914.8,249.93 2938.8,248.22 2961.4,247 2983.9,245.79 3755.7,245.09 3771.4,229 3777.6,222.65 3777.4,\ -213.61 3774.9,204.95", + lp="5481.4,221.5", + pos="e,5454.9,194.34 3800.6,251.67 3824.1,249.79 3848.5,248.11 3871.4,247 3893.4,245.93 5444.9,244.69 5460.4,229 5467.3,221.97 5465.2,\ +212.13 5460.4,203.04", style=solid]; category [height=0.5, - pos="3862.4,178", + pos="5542.4,178", width=1.4263]; "case to phenotypic feature association" -> category [color=blue, label=category, - lp="3866.9,221.5", - pos="e,3851.3,195.84 2891.7,251.77 2914.8,249.91 2938.8,248.21 2961.4,247 3008.7,244.47 3769.9,247.8 3813.4,229 3825.8,223.65 3836.6,\ -213.54 3844.9,203.81", + lp="5552.9,221.5", + pos="e,5533.8,195.81 3800.3,251.69 3823.9,249.8 3848.4,248.11 3871.4,247 3916.6,244.81 5460.6,248.59 5501.4,229 5512.4,223.72 5521.4,\ +213.91 5528.2,204.36", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="4016.4,178", + pos="5696.4,178", width=2.3651]; "case to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="4016.4,221.5", - pos="e,3988.4,195.01 2891.4,251.76 2914.7,249.89 2938.7,248.19 2961.4,247 3065.8,241.52 3800.3,251.44 3902.4,229 3929.2,223.1 3957.5,\ -210.72 3979.2,199.76", + lp="5700.4,221.5", + pos="e,5669.6,195.33 3800.3,251.68 3823.9,249.79 3848.4,248.11 3871.4,247 3966.7,242.42 5495.3,250.01 5588.4,229 5613.7,223.28 5640.2,\ +211.11 5660.6,200.22", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4195.4,178", + pos="5875.4,178", width=2.1123]; "case to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4192.4,221.5", - pos="e,4169.3,195.04 2891.1,251.72 2914.5,249.85 2938.7,248.16 2961.4,247 3086.5,240.64 3966.4,257.13 4088.4,229 4113.7,223.17 4140.1,\ -210.88 4160.4,199.94", + lp="5875.4,221.5", + pos="e,5850.3,195.09 3800.3,251.66 3823.9,249.77 3848.4,248.09 3871.4,247 3976.9,241.98 5669.6,253.15 5772.4,229 5796.8,223.27 5822.1,\ +211.06 5841.6,200.15", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4325.4,178", + pos="6005.4,178", width=1.011]; "case to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4337.9,221.5", - pos="e,4310.3,194.5 2890.9,251.7 2914.3,249.82 2938.6,248.14 2961.4,247 3033.3,243.42 4189.1,251.92 4257.4,229 4274.3,223.34 4290.4,211.8 \ -4302.8,201.23", + lp="6019.9,221.5", + pos="e,5990.6,195.01 3800,251.67 3823.7,249.77 3848.3,248.09 3871.4,247 3928.8,244.29 5886.1,247.74 5940.4,229 5956.4,223.49 5971.5,212.35 \ +5983.1,201.98", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="4453.4,178", + pos="6133.4,178", width=2.0401]; "case to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="4463.4,221.5", - pos="e,4439,195.95 2890.6,251.7 2914.1,249.81 2938.5,248.13 2961.4,247 3040.9,243.09 4318.8,256.55 4393.4,229 4407.9,223.63 4421.4,213.1 \ -4432,203.07", + lp="6144.4,221.5", + pos="e,6119.6,195.96 3800,251.66 3823.7,249.76 3848.3,248.08 3871.4,247 3932.6,244.13 6018.1,250.56 6075.4,229 6089.5,223.7 6102.4,213.32 \ +6112.5,203.38", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="4589.4,178", + pos="6269.4,178", width=1.2277]; "case to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="4579.4,221.5", - pos="e,4571.6,194.54 2890.6,251.68 2914.1,249.8 2938.5,248.12 2961.4,247 3047.4,242.81 4428.9,253.69 4511.4,229 4530.5,223.29 4549.3,\ -211.43 4563.7,200.68", + lp="6259.4,221.5", + pos="e,6251.9,194.56 3800,251.65 3823.7,249.76 3848.3,248.08 3871.4,247 3935.8,243.99 6130.6,247.55 6192.4,229 6211.1,223.38 6229.5,211.68 \ +6243.7,201.01", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="4695.4,178", + pos="6375.4,178", width=1.2277]; "case to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="4681.9,221.5", - pos="e,4677.9,194.55 2890.3,251.69 2913.9,249.8 2938.4,248.11 2961.4,247 3053.3,242.56 4530.3,255.62 4618.4,229 4637.1,223.35 4655.5,\ -211.65 4669.7,200.99", + lp="6361.9,221.5", + pos="e,6357.9,194.57 3800,251.64 3823.7,249.75 3848.3,248.08 3871.4,247 3938.7,243.86 6233.8,248.39 6298.4,229 6317.1,223.38 6335.5,211.68 \ +6349.7,201.01", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="4799.4,178", + pos="6479.4,178", width=1.1735]; "case to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="4796.4,221.5", - pos="e,4780.9,194.32 2890.3,251.67 2913.9,249.79 2938.4,248.1 2961.4,247 3058.8,242.32 4623.6,255.86 4717.4,229 4737.4,223.28 4757.3,\ -211.29 4772.5,200.49", + lp="6476.4,221.5", + pos="e,6460.9,194.34 3800,251.64 3823.7,249.75 3848.3,248.07 3871.4,247 3941.5,243.75 6329.9,248.21 6397.4,229 6417.4,223.31 6437.3,211.32 \ +6452.5,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4906.4,178", + pos="6586.4,178", width=1.1735]; "case to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="4926.4,221.5", - pos="e,4892.2,195.47 2890.3,251.66 2913.9,249.78 2938.4,248.1 2961.4,247 3013.7,244.51 4796.2,246.85 4845.4,229 4860.3,223.59 4874.2,\ -212.83 4885,202.68", + lp="6606.4,221.5", + pos="e,6572.2,195.49 3800,251.63 3823.7,249.74 3848.3,248.07 3871.4,247 3945,243.59 6456.1,254.05 6525.4,229 6540.3,223.61 6554.2,212.85 \ +6565,202.7", style=solid]; subject -> object [label=relation, lp="1719.4,134.5", @@ -342,11 +454,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3008.4,265", + pos="3918.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3139.4,265", + pos="4049.4,265", width=2.0762]; } diff --git a/graphviz/case_to_phenotypic_feature_association.svg b/graphviz/case_to_phenotypic_feature_association.svg index 1a473b887e..3c1c5b0a60 100644 --- a/graphviz/case_to_phenotypic_feature_association.svg +++ b/graphviz/case_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + case to phenotypic feature association - -case to phenotypic feature association + +case to phenotypic feature association @@ -24,9 +24,9 @@ case to phenotypic feature association->association - + -is_a +is_a @@ -37,9 +37,9 @@ case to phenotypic feature association->entity to phenotypic feature association mixin - - -uses + + +uses @@ -50,8 +50,8 @@ case to phenotypic feature association->case to entity association mixin - - + + uses @@ -63,7 +63,7 @@ case to phenotypic feature association->id - + id @@ -76,7 +76,7 @@ case to phenotypic feature association->iri - + iri @@ -89,8 +89,8 @@ case to phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ case to phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ case to phenotypic feature association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ case to phenotypic feature association->subject - - + + subject @@ -141,8 +141,8 @@ case to phenotypic feature association->predicate - - + + predicate @@ -154,7 +154,7 @@ case to phenotypic feature association->object - + object @@ -167,9 +167,9 @@ case to phenotypic feature association->negated - - -negated + + +negated @@ -180,9 +180,9 @@ case to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -193,9 +193,9 @@ case to phenotypic feature association->publications - - -publications + + +publications @@ -206,9 +206,9 @@ case to phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -219,9 +219,9 @@ case to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -232,9 +232,9 @@ case to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -245,9 +245,9 @@ case to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -258,9 +258,9 @@ case to phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -271,9 +271,9 @@ case to phenotypic feature association->original subject - - -original subject + + +original subject @@ -284,9 +284,9 @@ case to phenotypic feature association->original predicate - - -original predicate + + +original predicate @@ -297,176 +297,319 @@ case to phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +case to phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +case to phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +case to phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +case to phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +case to phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +case to phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +case to phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +case to phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +case to phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +case to phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +case to phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + case to phenotypic feature association->type - - -type + + +type - + category - -category + +category - + case to phenotypic feature association->category - - -category + + +category - + frequency qualifier - -frequency value + +frequency value - + case to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + case to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + case to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier - + sex qualifier - -biological sex + +biological sex - + case to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier - + has count - -integer + +integer - + case to phenotypic feature association->has count - - -has count + + +has count - + has total - -integer + +integer - + case to phenotypic feature association->has total - - -has total + + +has total - + has quotient - -double + +double - + case to phenotypic feature association->has quotient - - -has quotient + + +has quotient - + has percentage - -double + +double - + case to phenotypic feature association->has percentage - - -has percentage + + +has percentage - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/cell_line_as_a_model_of_disease_association.gv b/graphviz/cell_line_as_a_model_of_disease_association.gv index d27b1b9836..5b3cb6781b 100644 --- a/graphviz/cell_line_as_a_model_of_disease_association.gv +++ b/graphviz/cell_line_as_a_model_of_disease_association.gv @@ -1,28 +1,28 @@ digraph { - graph [bb="0,0,4640.8,283"]; + graph [bb="0,0,6356.8,283"]; node [label="\N"]; "cell line as a model of disease association" [height=0.5, label="cell line as a model of disease association", - pos="2627.8,265", + pos="3603.8,265", width=5.6509]; "cell line to disease or phenotypic feature association" [height=0.5, pos="254.78,178", width=7.0771]; "cell line as a model of disease association" -> "cell line to disease or phenotypic feature association" [label=is_a, - lp="1016.8,221.5", - pos="e,416.62,191.94 2426,262.58 2118.6,259.76 1515,251.62 1002.8,229 805.13,220.27 578.48,204.28 426.95,192.73"]; + lp="1010.8,221.5", + pos="e,412.78,192.12 3401.9,262.7 2874.5,259.07 1463.9,247.86 996.78,229 799.57,221.04 573.32,204.76 423.02,192.93"]; "model to disease association mixin" [height=0.5, pos="699.78,178", width=4.7843]; "cell line as a model of disease association" -> "model to disease association mixin" [label=uses, - lp="1237.3,221.5", - pos="e,809.88,191.85 2424.9,263.46 2151.2,261.69 1648.8,254.83 1220.8,229 1083,220.69 925.4,204.64 819.92,192.97"]; + lp="1228.3,221.5", + pos="e,807.45,192.13 3401.1,263.19 2904.1,260.87 1635,252.72 1211.8,229 1076.3,221.41 921.27,205.21 817.63,193.3"]; "entity to disease association mixin" [height=0.5, pos="1060.8,178", width=4.7482]; "cell line as a model of disease association" -> "entity to disease association mixin" [label=uses, lp="1383.3,221.5", - pos="e,1136.2,194.22 2427.6,261.72 2125.3,257.72 1566.3,247.99 1366.8,229 1291.8,221.86 1207.3,207.59 1146.2,196.11"]; + pos="e,1134.9,194.23 3400.2,264.63 2925.9,265.47 1757.8,263.81 1366.8,229 1291.2,222.27 1206.1,207.8 1144.9,196.15"]; id [color=blue, height=0.5, label=string, @@ -30,9 +30,9 @@ digraph { width=1.0652]; "cell line as a model of disease association" -> id [color=blue, label=id, - lp="1499.8,221.5", - pos="e,1316.8,189.97 2427,262.07 2150.7,258.67 1667.5,249.9 1492.8,229 1422,220.53 1404.4,215.28 1335.8,196 1332.7,195.13 1329.5,194.16 \ -1326.3,193.14", + lp="1500.8,221.5", + pos="e,1316.8,189.97 3401.4,262.82 2909.8,259.66 1679.5,249.75 1493.8,229 1422.5,221.04 1404.9,215.35 1335.8,196 1332.7,195.13 1329.5,\ +194.16 1326.3,193.14", style=solid]; iri [color=blue, height=0.5, @@ -41,9 +41,8 @@ digraph { width=1.2277]; "cell line as a model of disease association" -> iri [color=blue, label=iri, - lp="1602.8,221.5", - pos="e,1421.7,190.11 2428.1,261.47 2174.3,257.52 1750.3,248.25 1594.8,229 1525.7,220.45 1509,213.98 1441.8,196 1438.4,195.1 1434.9,194.11 \ -1431.5,193.09", + lp="1597.8,221.5", + pos="e,1422.1,190.02 3401.5,262.8 2926.3,259.66 1765.8,249.93 1589.8,229 1534.3,222.4 1472.2,205.4 1431.8,193.05", style=solid]; name [color=blue, height=0.5, @@ -52,8 +51,8 @@ digraph { width=1.5707]; "cell line as a model of disease association" -> name [color=blue, label=name, - lp="1694.8,221.5", - pos="e,1542.7,192.29 2426,262.59 2190,259.89 1813.9,252 1674.8,229 1632.2,221.97 1585.3,207.28 1552.1,195.64", + lp="1693.8,221.5", + pos="e,1542.1,192.37 3400.9,263.47 2939.8,261.8 1840.5,255.11 1673.8,229 1631.5,222.37 1584.9,207.67 1551.9,195.91", style=solid]; description [color=blue, height=0.5, @@ -62,8 +61,8 @@ digraph { width=2.0943]; "cell line as a model of disease association" -> description [color=blue, label=description, - lp="1799.3,221.5", - pos="e,1682.8,195.09 2430.9,260.4 2194.5,255.4 1821.9,245.11 1758.8,229 1735.2,222.97 1710.6,210.96 1691.6,200.23", + lp="1797.3,221.5", + pos="e,1682.2,195.26 3402,262.59 2939.2,259.02 1835.3,248.5 1756.8,229 1733.5,223.22 1709.4,211.22 1690.8,200.42", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,7 +72,7 @@ digraph { "cell line as a model of disease association" -> "has attribute" [color=blue, label="has attribute", lp="1916.8,221.5", - pos="e,1818.7,195.29 2429.8,260.86 2222.9,256.61 1921.1,247.36 1869.8,229 1853.8,223.28 1838.4,212.34 1826.4,202.15", + pos="e,1818.4,195.2 3401,263.21 2958.6,261.05 1941,253.43 1869.8,229 1853.6,223.45 1838.1,212.42 1826.1,202.13", style=solid]; predicate [color=blue, height=0.5, @@ -83,18 +82,18 @@ digraph { "cell line as a model of disease association" -> predicate [color=blue, label=predicate, lp="2016.8,221.5", - pos="e,1956.9,196.02 2426.7,262.23 2251.8,259.21 2020.6,251.03 1982.8,229 1973.5,223.61 1966.5,214.35 1961.4,205.26", + pos="e,1956.8,196.14 3400,264.68 2978.2,265.39 2043.5,263.07 1982.8,229 1973.3,223.7 1966.3,214.34 1961.2,205.14", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="4026.8,91", + pos="5742.8,91", width=1.9318]; "cell line as a model of disease association" -> object [color=blue, label=object, lp="2095.8,178", - pos="e,3957,91.747 2460.2,254.73 2306.4,244.44 2098.8,225.31 2073.8,196 2063.4,183.82 2062.7,171.51 2073.8,160 2139.8,91.603 3588.4,90.853 \ -3947,91.721", + pos="e,5673.3,91.949 3403.7,261.67 3091.4,257.52 2502.1,247.5 2292.8,229 2191.1,220.02 2002.3,232.83 2073.8,160 2138.9,93.7 5133.2,91.768 \ +5663.1,91.946", style=solid]; negated [color=blue, height=0.5, @@ -103,9 +102,8 @@ digraph { width=1.2999]; "cell line as a model of disease association" -> negated [color=blue, label=negated, - lp="2367.8,221.5", - pos="e,2209,189.93 2487.7,251.91 2440.2,246.52 2386.9,239.05 2338.8,229 2288.8,218.56 2277.6,210.87 2228.8,196 2225.5,194.99 2222.1,193.95 \ -2218.6,192.9", + lp="2403.8,221.5", + pos="e,2208.5,190.32 3401.5,262.99 3105.1,260.7 2567.1,253.24 2374.8,229 2320,222.1 2258.7,205.5 2218.3,193.31", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +112,8 @@ digraph { width=2.1304]; "cell line as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2476.3,221.5", - pos="e,2348.7,194.24 2530.5,249.09 2502,243.78 2470.9,237.08 2442.8,229 2413.9,220.71 2382.5,208.5 2358,198.21", + lp="2538.3,221.5", + pos="e,2357.2,193.12 3401.6,263.01 3132.7,260.74 2671.8,253.32 2504.8,229 2457.4,222.1 2404.8,207.72 2367,196.15", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +122,8 @@ digraph { width=1.7332]; "cell line as a model of disease association" -> publications [color=blue, label=publications, - lp="2579.8,221.5", - pos="e,2489.8,195.45 2576.4,247.56 2562.8,242.39 2548.4,236.13 2535.8,229 2522.3,221.42 2508.7,211.19 2497.5,201.95", + lp="2677.8,221.5", + pos="e,2507.2,192.88 3401.5,262.95 3161.5,260.6 2775.9,253.07 2633.8,229 2593.3,222.14 2548.8,207.9 2516.7,196.37", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,8 +132,8 @@ digraph { width=2.0943]; "cell line as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2674.3,221.5", - pos="e,2627.8,196.18 2627.8,246.8 2627.8,235.16 2627.8,219.55 2627.8,206.24", + lp="2827.3,221.5", + pos="e,2663.8,193.89 3403.7,261.75 3199.2,258.32 2895.7,249.82 2780.8,229 2743.7,222.28 2703.2,208.76 2673.2,197.47", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -144,8 +142,8 @@ digraph { width=3.015]; "cell line as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2822.3,221.5", - pos="e,2797.5,195.37 2676.5,247.48 2692,241.92 2709.2,235.48 2724.8,229 2746.1,220.11 2769.3,209.19 2788.5,199.83", + lp="2971.3,221.5", + pos="e,2849.2,195.77 3410.2,259.43 3220.6,254.13 2953.5,244.12 2906.8,229 2888.9,223.23 2871.2,212.21 2857.3,201.98", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -154,8 +152,8 @@ digraph { width=3.015]; "cell line as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3044.8,221.5", - pos="e,3018.4,194.37 2754.8,250.93 2798.2,245.46 2846.8,238.19 2890.8,229 2930.7,220.66 2974.8,207.94 3008.6,197.41", + lp="3138.8,221.5", + pos="e,3049.1,195.98 3414.8,258.3 3257.3,252.59 3056.6,242.69 3043.8,229 3037.4,222.18 3039.1,213.11 3043.6,204.57", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -164,9 +162,8 @@ digraph { width=3.015]; "cell line as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3307.3,221.5", - pos="e,3260.1,194.78 2771,252.17 2794.3,250.36 2818.2,248.57 2840.8,247 2975.4,237.63 3011.2,253.78 3143.8,229 3180.4,222.16 3220.3,209.26 \ -3250.6,198.27", + lp="3348.3,221.5", + pos="e,3261.4,194.99 3421.2,257.02 3337.9,251.91 3254.7,243.29 3241.8,229 3232.5,218.83 3240.2,208.72 3252.7,200.28", style=solid]; timepoint [color=blue, height=0.5, @@ -175,9 +172,8 @@ digraph { width=1.5346]; "cell line as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3476.8,221.5", - pos="e,3463.7,195.25 2767.5,251.88 2791.9,250.03 2817.1,248.31 2840.8,247 2904.8,243.45 3357.5,250.83 3417.8,229 3426.2,225.95 3442,213.61 \ -3455.8,201.96", + lp="3496.8,221.5", + pos="e,3467.2,195.52 3506.1,249.11 3485.7,243.97 3468.3,237.34 3461.8,229 3456.1,221.76 3457.7,212.7 3461.9,204.28", style=solid]; "original subject" [color=blue, height=0.5, @@ -187,8 +183,7 @@ digraph { "cell line as a model of disease association" -> "original subject" [color=blue, label="original subject", lp="3593.8,221.5", - pos="e,3571.6,192.7 2766.9,251.83 2791.5,249.98 2816.9,248.27 2840.8,247 2915.6,243.02 3443.3,251.3 3514.8,229 3526.4,225.37 3527.5,220.57 \ -3537.8,214 3545.9,208.79 3554.8,203.21 3563,198.07", + pos="e,3565.1,190.29 3556.6,247.32 3549.1,242.57 3542.3,236.56 3537.8,229 3529.7,215.65 3541.4,203.87 3556.2,195.09", style=solid]; "original predicate" [color=blue, height=0.5, @@ -197,9 +192,8 @@ digraph { width=1.5887]; "cell line as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3735.3,221.5", - pos="e,3691.5,195.26 2766.3,251.78 2791.1,249.93 2816.7,248.23 2840.8,247 2885.7,244.71 3607.8,245.12 3649.8,229 3657.6,226 3671.7,213.86 \ -3684.1,202.3", + lp="3731.3,221.5", + pos="e,3689.5,195.28 3626.9,246.83 3634.3,241.23 3642.4,234.94 3649.8,229 3660.5,220.35 3672,210.53 3681.9,201.9", style=solid]; "original object" [color=blue, height=0.5, @@ -208,93 +202,212 @@ digraph { width=1.0652]; "cell line as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3864.3,221.5", - pos="e,3819.1,195.96 2765.8,251.75 2790.7,249.89 2816.5,248.2 2840.8,247 2867.4,245.69 3777.6,243.77 3799.8,229 3807.8,223.65 3812.9,\ -214.66 3816.2,205.77", + lp="3863.3,221.5", + pos="e,3818.3,195.93 3728.7,250.75 3759.3,245.49 3786.6,238.39 3798.8,229 3806.4,223.14 3811.5,214.2 3815,205.49", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3954.8,178", + width=2.1304]; + "cell line as a model of disease association" -> "subject category" [color=blue, + label="subject category", + lp="3995.3,221.5", + pos="e,3947,196.33 3753.8,252.81 3827.6,246.32 3903.8,237.73 3918.8,229 3928.3,223.42 3936.1,214.17 3941.8,205.14", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="4125.8,178", + width=2.1304]; + "cell line as a model of disease association" -> "object category" [color=blue, + label="object category", + lp="4141.3,221.5", + pos="e,4109.2,195.62 3748.7,252.33 3771.5,250.52 3794.8,248.7 3816.8,247 3870.5,242.85 4008.3,247.88 4058.8,229 4074.5,223.14 4089.6,\ +212.4 4101.5,202.38", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4258.8,178", + width=1.0652]; + "cell line as a model of disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="4277.3,221.5", + pos="e,4243,194.68 3745.2,252.06 3769.1,250.23 3793.6,248.47 3816.8,247 3859.4,244.3 4161.1,244.81 4200.8,229 4208.7,225.86 4223.1,213.44 \ +4235.6,201.77", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4354.8,178", + width=1.0652]; + "cell line as a model of disease association" -> "object closure" [color=blue, + label="object closure", + lp="4395.8,221.5", + pos="e,4352.3,196.37 3743.8,251.93 3768.1,250.09 3793.2,248.35 3816.8,247 3845.5,245.36 4310.1,245.32 4333.8,229 4341.5,223.64 4346.5,\ +214.81 4349.5,206.05", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4487.8,178", + width=2.1304]; + "cell line as a model of disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4554.3,221.5", + pos="e,4479.8,196.2 3742.9,251.86 3767.5,250.01 3792.9,248.29 3816.8,247 3851.9,245.1 4418.5,245.08 4449.8,229 4460.1,223.71 4468.4,214.22 \ +4474.5,204.92", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4676.8,178", + width=2.1304]; + "cell line as a model of disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4744.3,221.5", + pos="e,4671.1,196.13 3742.1,251.79 3766.9,249.93 3792.6,248.23 3816.8,247 3862.8,244.67 4605.8,251.84 4645.8,229 4655,223.74 4661.8,214.51 \ +4666.7,205.4", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4866.8,178", + width=1.0652]; + "cell line as a model of disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4916.8,221.5", + pos="e,4859.8,196.2 3741.8,251.73 3766.7,249.87 3792.5,248.18 3816.8,247 3844.9,245.63 4806.9,242.24 4831.8,229 4841.6,223.77 4849.3,\ +214.42 4854.9,205.21", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="5025.8,178", + width=1.0652]; + "cell line as a model of disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="5069.8,221.5", + pos="e,5018.4,195.75 3741.5,251.71 3766.5,249.84 3792.4,248.16 3816.8,247 3849.3,245.45 4959.8,243.88 4988.8,229 4999.1,223.69 5007.3,\ +214.01 5013.3,204.57", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="5176.8,178", + width=1.0652]; + "cell line as a model of disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5229.8,221.5", + pos="e,5168.8,195.78 3741.2,251.69 3766.3,249.82 3792.3,248.14 3816.8,247 3853.4,245.29 5104.9,245.32 5137.8,229 5148.5,223.68 5157.1,\ +213.86 5163.5,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5347.8,178", + width=1.0652]; + "cell line as a model of disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="5395.3,221.5", + pos="e,5339.5,195.8 3740.9,251.68 3766.1,249.81 3792.2,248.13 3816.8,247 3858.2,245.1 5270.6,247.17 5307.8,229 5318.6,223.7 5327.5,213.88 \ +5334.1,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5491.8,178", + width=2.347]; + "cell line as a model of disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5551.3,221.5", + pos="e,5488.8,196.01 3740.6,251.68 3765.9,249.8 3792.1,248.12 3816.8,247 3862.6,244.92 5430.3,253.97 5468.8,229 5476.9,223.71 5482.2,\ +214.73 5485.7,205.83", style=solid]; type [height=0.5, - pos="3909.8,178", + pos="5625.8,178", width=0.86659]; "cell line as a model of disease association" -> type [color=blue, label=type, - lp="3941.8,221.5", - pos="e,3919.7,195.52 2765.5,251.73 2790.5,249.87 2816.4,248.17 2840.8,247 2870.7,245.56 3898.8,250.37 3919.8,229 3926,222.67 3925.8,213.63 \ -3923.3,204.97", + lp="5647.8,221.5", + pos="e,5630.9,196.18 3740.6,251.66 3765.9,249.78 3792.1,248.1 3816.8,247 3841.9,245.88 5606.9,246.67 5624.8,229 5630.7,223.09 5632.3,\ +214.52 5632,206.13", style=solid]; category [height=0.5, - pos="4010.8,178", + pos="5726.8,178", width=1.4263]; "cell line as a model of disease association" -> category [color=blue, label=category, - lp="4015.3,221.5", - pos="e,3999.7,195.86 2765.5,251.72 2790.5,249.86 2816.4,248.17 2840.8,247 2903,244.02 3904.5,253.59 3961.8,229 3974.2,223.68 3985,213.58 \ -3993.3,203.84", + lp="5725.3,221.5", + pos="e,5713.2,195.46 3740.6,251.66 3765.9,249.78 3792.1,248.1 3816.8,247 3868.1,244.7 5619.6,246.94 5667.8,229 5682.4,223.57 5695.8,212.81 \ +5706.2,202.66", style=solid]; subject [height=0.5, - pos="4124.8,178", + pos="5840.8,178", width=1.2277]; "cell line as a model of disease association" -> subject [color=blue, label=subject, - lp="4107.8,221.5", - pos="e,4107.8,194.76 2765.2,251.72 2790.3,249.85 2816.3,248.16 2840.8,247 2907.9,243.82 3986.6,249.16 4050.8,229 4068.8,223.34 4086.4,\ -211.76 4099.9,201.16", + lp="5819.8,221.5", + pos="e,5822.5,194.56 3740.6,251.65 3765.9,249.77 3792.1,248.1 3816.8,247 3870.7,244.6 5708.9,244.13 5760.8,229 5780.2,223.32 5799.6,211.46 \ +5814.4,200.71", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="4271.8,178", + pos="5987.8,178", width=2.3651]; "cell line as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="4258.8,221.5", - pos="e,4239.4,194.69 2765.2,251.7 2790.3,249.83 2816.3,248.14 2840.8,247 2984.7,240.26 3996.1,255.58 4137.8,229 4169.8,222.98 4204.3,\ -209.98 4230.2,198.74", + lp="5972.8,221.5", + pos="e,5954.6,194.62 3740.6,251.64 3765.9,249.76 3792.1,248.09 3816.8,247 3929.6,242 5738.6,249.02 5849.8,229 5882.8,223.05 5918.4,209.97 \ +5945.2,198.68", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4450.8,178", + pos="6166.8,178", width=2.1123]; "cell line as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4439.8,221.5", - pos="e,4421.7,194.83 2764.9,251.68 2790.1,249.81 2816.2,248.13 2840.8,247 2923.5,243.2 4249.7,245.73 4330.8,229 4359.3,223.11 4389.6,\ -210.43 4412.6,199.31", + lp="6154.8,221.5", + pos="e,6137.2,194.87 3740.3,251.64 3765.7,249.76 3792,248.09 3816.8,247 3940.4,241.57 5923.4,253.41 6044.8,229 6073.8,223.17 6104.6,210.49 \ +6128,199.36", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4587.8,178", + pos="6303.8,178", width=1.011]; "cell line as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4589.3,221.5", - pos="e,4569.7,193.83 2764.6,251.68 2789.9,249.8 2816.1,248.12 2840.8,247 2933.1,242.82 4415.8,254.24 4504.8,229 4525.4,223.15 4546,210.74 \ -4561.6,199.74", + lp="6305.3,221.5", + pos="e,6285.4,193.86 3740.3,251.63 3765.7,249.75 3792,248.08 3816.8,247 3883.5,244.09 6155.5,246.95 6219.8,229 6240.6,223.19 6261.5,210.78 \ +6277.3,199.77", style=solid]; relation [height=0.5, - pos="4075.8,18", + pos="5791.8,18", width=1.2999]; - object -> relation [pos="e,4064.2,35.705 4038.4,73.174 4044.4,64.509 4051.8,53.768 4058.4,44.141", + object -> relation [pos="e,5780.2,35.705 5754.4,73.174 5760.4,64.509 5767.8,53.768 5774.4,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="2887.8,265", + pos="3863.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3018.8,265", + pos="3994.8,265", width=2.0762]; subject -> object [label=relation, - lp="4082.8,134.5", - pos="e,4033.2,108.97 4092.3,165.59 4079.5,159.94 4065.4,152.13 4054.8,142 4047.8,135.31 4042,126.48 4037.6,118.1"]; - subject -> relation [pos="e,4087,35.828 4123.4,159.99 4121.3,139.02 4116.4,102.55 4105.8,73 4102.3,63.258 4097.2,53.189 4092.1,44.423", + lp="5798.8,134.5", + pos="e,5749.2,108.97 5808.3,165.59 5795.5,159.94 5781.4,152.13 5770.8,142 5763.8,135.31 5758,126.48 5753.6,118.1"]; + subject -> relation [pos="e,5803,35.828 5839.4,159.99 5837.3,139.02 5832.4,102.55 5821.8,73 5818.3,63.258 5813.2,53.189 5808.1,44.423", style=dotted]; "cell line as a model of disease association_subject" [color=blue, height=0.5, label="cell line", - pos="3158.8,265", + pos="4134.8,265", width=1.2999]; } diff --git a/graphviz/cell_line_as_a_model_of_disease_association.svg b/graphviz/cell_line_as_a_model_of_disease_association.svg index 3855ab432d..916e1aa193 100644 --- a/graphviz/cell_line_as_a_model_of_disease_association.svg +++ b/graphviz/cell_line_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + cell line as a model of disease association - -cell line as a model of disease association + +cell line as a model of disease association @@ -24,9 +24,9 @@ cell line as a model of disease association->cell line to disease or phenotypic feature association - - -is_a + + +is_a @@ -37,9 +37,9 @@ cell line as a model of disease association->model to disease association mixin - - -uses + + +uses @@ -50,8 +50,8 @@ cell line as a model of disease association->entity to disease association mixin - - + + uses @@ -63,9 +63,9 @@ cell line as a model of disease association->id - - -id + + +id @@ -76,9 +76,9 @@ cell line as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ cell line as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ cell line as a model of disease association->description - - -description + + +description @@ -115,8 +115,8 @@ cell line as a model of disease association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ cell line as a model of disease association->predicate - - + + predicate object - -named thing + +named thing cell line as a model of disease association->object - - + + object @@ -154,9 +154,9 @@ cell line as a model of disease association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ cell line as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ cell line as a model of disease association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ cell line as a model of disease association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ cell line as a model of disease association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ cell line as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ cell line as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ cell line as a model of disease association->timepoint - - -timepoint + + +timepoint @@ -258,8 +258,8 @@ cell line as a model of disease association->original subject - - + + original subject @@ -271,9 +271,9 @@ cell line as a model of disease association->original predicate - - -original predicate + + +original predicate @@ -284,130 +284,273 @@ cell line as a model of disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +cell line as a model of disease association->subject category + + +subject category + + + +object category + +ontology class + + + +cell line as a model of disease association->object category + + +object category + + + +subject closure + +string + + + +cell line as a model of disease association->subject closure + + +subject closure + + + +object closure + +string + + + +cell line as a model of disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +cell line as a model of disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +cell line as a model of disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +cell line as a model of disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +cell line as a model of disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +cell line as a model of disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +cell line as a model of disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +cell line as a model of disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + cell line as a model of disease association->type - - -type + + +type - + category - -category + +category - + cell line as a model of disease association->category - - -category + + +category - + subject - -subject + +subject - + cell line as a model of disease association->subject - - -subject + + +subject - + frequency qualifier - -frequency value + +frequency value - + cell line as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + cell line as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + cell line as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + relation - -relation + +relation - + object->relation - - + + - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + subject->relation - - + + - + cell line as a model of disease association_subject - -cell line + +cell line diff --git a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv index 51a47e8d16..79787e2840 100644 --- a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv @@ -1,30 +1,30 @@ digraph { - graph [bb="0,0,4010.6,283"]; + graph [bb="0,0,5726.6,283"]; node [label="\N"]; "cell line to disease or phenotypic feature association" [height=0.5, label="cell line to disease or phenotypic feature association", - pos="2216.4,265", + pos="3267.4,265", width=7.0771]; association [height=0.5, pos="62.394,178", width=1.7332]; "cell line to disease or phenotypic feature association" -> association [label=is_a, lp="717.39,221.5", - pos="e,106.47,190.83 1968,260.9 1668.2,256.54 1148.7,247.04 703.39,229 449.84,218.73 384.44,233.02 133.39,196 127.91,195.19 122.22,194.16 \ -116.57,193.01"]; + pos="e,106.47,190.83 3012.6,264.25 2551.6,263.86 1548.7,259.22 703.39,229 449.8,219.93 384.44,233.02 133.39,196 127.91,195.19 122.22,\ +194.16 116.57,193.01"]; "cell line to entity association mixin" [height=0.5, pos="315.39,178", width=4.8024]; "cell line to disease or phenotypic feature association" -> "cell line to entity association mixin" [label=uses, lp="1023.9,221.5", - pos="e,436.75,190.82 1973.4,259.51 1729.2,254.4 1342.1,244.67 1007.4,229 780.5,218.38 723.83,213.9 497.39,196 481,194.7 463.78,193.24 \ + pos="e,436.75,190.82 3012.7,264.13 2594,263.43 1734.5,258.14 1007.4,229 780.44,219.91 723.83,213.9 497.39,196 481,194.7 463.78,193.24 \ 446.75,191.72"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="780.39,178", width=7.6188]; "cell line to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, lp="1206.9,221.5", - pos="e,887.18,194.61 1966.2,261.56 1758.3,258.07 1454.7,249.59 1190.4,229 1091.2,221.28 979.15,207.24 897.27,196"]; + pos="e,884.16,194.7 3014.1,263.05 2540.5,260.71 1537.4,253.01 1190.4,229 1090,222.05 976.37,207.68 894.27,196.13"]; id [color=blue, height=0.5, label=string, @@ -33,7 +33,7 @@ digraph { "cell line to disease or phenotypic feature association" -> id [color=blue, label=id, lp="1324.4,221.5", - pos="e,1140.4,189.97 1975.3,259.15 1753.1,253.85 1439.8,244.05 1317.4,229 1246.2,220.24 1228.5,215.35 1159.4,196 1156.3,195.13 1153.1,\ + pos="e,1140.4,189.97 3015.5,262.12 2526.3,258.09 1481.4,247.43 1317.4,229 1246.1,220.99 1228.5,215.35 1159.4,196 1156.3,195.13 1153.1,\ 194.16 1149.9,193.14", style=solid]; iri [color=blue, @@ -43,9 +43,8 @@ digraph { width=1.2277]; "cell line to disease or phenotypic feature association" -> iri [color=blue, label=iri, - lp="1428.4,221.5", - pos="e,1245.3,190.13 1962.3,263.54 1805.5,260.6 1600.7,251.99 1420.4,229 1350.5,220.09 1333.5,214.11 1265.4,196 1262,195.1 1258.6,194.12 \ -1255.1,193.1", + lp="1421.4,221.5", + pos="e,1245.7,190.01 3015.7,262.05 2545.6,258.01 1567.8,247.48 1413.4,229 1357.9,222.36 1295.8,205.37 1255.5,193.03", style=solid]; name [color=blue, height=0.5, @@ -54,8 +53,8 @@ digraph { width=1.5707]; "cell line to disease or phenotypic feature association" -> name [color=blue, label=name, - lp="1521.4,221.5", - pos="e,1367,192.15 1978.9,258.41 1807.1,253.22 1590.1,243.99 1501.4,229 1458.2,221.7 1410.4,207.04 1376.6,195.48", + lp="1517.4,221.5", + pos="e,1365.7,192.35 3014.2,262.81 2560.5,260.11 1642.7,251.88 1497.4,229 1455.1,222.34 1408.5,207.64 1375.5,195.89", style=solid]; description [color=blue, height=0.5, @@ -64,8 +63,8 @@ digraph { width=2.0943]; "cell line to disease or phenotypic feature association" -> description [color=blue, label=description, - lp="1622.9,221.5", - pos="e,1506.8,195.22 1969.5,260.52 1823.5,256.48 1653.7,247.77 1582.4,229 1559,222.84 1534.6,210.95 1515.7,200.31", + lp="1620.9,221.5", + pos="e,1505.8,195.24 3016.6,261.72 2563.4,257.19 1648.6,246 1580.4,229 1557.1,223.2 1533,211.2 1514.5,200.41", style=solid]; "has attribute" [color=blue, height=0.5, @@ -75,7 +74,7 @@ digraph { "cell line to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1740.4,221.5", - pos="e,1642.4,195.18 1968.9,260.7 1859.3,256.54 1743.9,247.65 1693.4,229 1677.5,223.11 1662.1,212.16 1650.1,202.01", + pos="e,1642,195.18 3015.1,262.4 2586,259.11 1754.6,250.06 1693.4,229 1677.2,223.43 1661.8,212.4 1649.8,202.11", style=solid]; predicate [color=blue, height=0.5, @@ -85,17 +84,18 @@ digraph { "cell line to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1840.4,221.5", - pos="e,1780.8,196.39 2010.3,254.4 1917.7,248.62 1824.9,240.18 1806.4,229 1797.4,223.54 1790.4,214.45 1785.4,205.5", + pos="e,1780.4,196.13 3012.6,264.07 2607.8,263.32 1857.9,257.98 1806.4,229 1797,223.69 1789.9,214.33 1784.8,205.13", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="3868.4,91", + pos="5584.4,91", width=1.9318]; "cell line to disease or phenotypic feature association" -> object [color=blue, label=object, lp="1919.4,178", - pos="e,3798.9,91.724 2024.9,253.12 1929.3,240.88 1844.3,214.93 1897.4,160 1964.1,90.926 3428.4,90.699 3788.8,91.695", + pos="e,5514.6,91.943 3022.5,260.03 2737.4,254.8 2284,244.42 2114.4,229 2013.6,219.84 1826.5,232.22 1897.4,160 1962.8,93.377 4971.8,91.711 \ +5504.3,91.938", style=solid]; negated [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { width=1.2999]; "cell line to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2140.4,221.5", - pos="e,2026.1,192.48 2163.2,247.31 2146.5,241.8 2128.1,235.42 2111.4,229 2085.7,219.12 2057.4,206.72 2035.5,196.74", + lp="2224.4,221.5", + pos="e,2032,190.37 3017.5,261.44 2751.5,257.72 2348.2,248.93 2195.4,229 2141.6,221.98 2081.4,205.49 2041.6,193.35", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=2.1304]; "cell line to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2215.9,221.5", - pos="e,2153.9,195.89 2200.6,246.8 2189.2,234.39 2173.7,217.46 2161,203.62", + lp="2356.9,221.5", + pos="e,2180.1,193.18 3018.5,261.14 2784.7,257.3 2452.2,248.53 2323.4,229 2277.5,222.05 2226.8,207.84 2190,196.34", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=1.7332]; "cell line to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2311.4,221.5", - pos="e,2282.2,195.62 2235.2,246.96 2241.2,241.37 2247.7,235.05 2253.4,229 2261,220.96 2268.9,211.79 2275.8,203.52", + lp="2494.4,221.5", + pos="e,2329.8,193.06 3019.6,260.68 2819.9,256.65 2555.6,247.87 2450.4,229 2412,222.11 2369.9,208.11 2339.3,196.67", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=2.0943]; "cell line to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2437.9,221.5", - pos="e,2426.1,195.08 2298.1,247.85 2318.4,242.79 2340,236.51 2359.4,229 2379.3,221.31 2400.3,210.17 2417.1,200.36", + lp="2639.9,221.5", + pos="e,2485.6,194.18 3028.1,258.78 2868.6,253.92 2674,244.94 2593.4,229 2559.4,222.29 2522.6,209.15 2495,198.02", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -144,8 +144,8 @@ digraph { width=3.015]; "cell line to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2608.9,221.5", - pos="e,2609.4,194.5 2359.7,250.08 2401.5,244.81 2447,237.88 2488.4,229 2526.2,220.9 2567.8,208.25 2599.8,197.7", + lp="2778.9,221.5", + pos="e,2668.6,196.17 3014.2,262.87 2895.6,259.33 2768.7,250.36 2714.4,229 2700,223.35 2686.5,212.99 2675.9,203.16", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -154,8 +154,8 @@ digraph { width=3.015]; "cell line to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2849.4,221.5", - pos="e,2836,193.85 2392.5,251.96 2510.5,243.67 2649.2,233.38 2677.4,229 2728,221.13 2784.4,207.5 2826.2,196.45", + lp="2945.4,221.5", + pos="e,2863.1,195.6 3035.1,257.56 2947,252.68 2864.3,244.09 2850.4,229 2842.8,220.79 2847.4,211.15 2855.6,202.54", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -164,9 +164,8 @@ digraph { width=3.015]; "cell line to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3118.9,221.5", - pos="e,3079.8,194.61 2392.8,252.01 2422.1,250.2 2452.1,248.46 2480.4,247 2688.3,236.31 2742.8,261.83 2948.4,229 2990,222.36 3035.7,209.07 \ -3070,197.86", + lp="3154.9,221.5", + pos="e,3072.6,194.03 3100.8,251.32 3076.6,246.2 3057,239.03 3048.4,229 3038,216.84 3047.9,206.43 3063.4,198.31", style=solid]; timepoint [color=blue, height=0.5, @@ -175,9 +174,8 @@ digraph { width=1.5346]; "cell line to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3296.4,221.5", - pos="e,3287.2,195.2 2390.3,251.8 2420.3,249.98 2451.3,248.29 2480.4,247 2563.6,243.32 3149.9,253.84 3229.4,229 3247.5,223.34 3265.3,211.99 \ -3279.2,201.53", + lp="3303.4,221.5", + pos="e,3283.3,194.53 3264.5,246.62 3263.6,236.66 3263.9,224.16 3268.4,214 3270.3,209.58 3273.2,205.46 3276.4,201.7", style=solid]; "original subject" [color=blue, height=0.5, @@ -186,9 +184,9 @@ digraph { width=1.0652]; "cell line to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3425.4,221.5", - pos="e,3399.2,194.01 2389.6,251.77 2419.8,249.94 2451,248.25 2480.4,247 2575.3,242.95 3244.2,255.65 3335.4,229 3355.5,223.14 3375.5,211.02 \ -3390.8,200.18", + lp="3417.4,221.5", + pos="e,3395.3,192.7 3304,247.02 3315.2,241.54 3327.4,235.26 3338.4,229 3349,222.96 3351.1,220.57 3361.4,214 3369.6,208.79 3378.4,203.21 \ +3386.7,198.07", style=solid]; "original predicate" [color=blue, height=0.5, @@ -197,71 +195,189 @@ digraph { width=1.5887]; "cell line to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3569.9,221.5", - pos="e,3521.2,195.83 2388.9,251.74 2419.4,249.9 2450.8,248.22 2480.4,247 2536.2,244.71 3434.5,251.9 3485.4,229 3497.2,223.69 3507.4,213.73 \ -3515.1,204.09", + lp="3556.9,221.5", + pos="e,3514.4,195.43 3410.4,250.1 3432.1,245.06 3453.8,238.23 3473.4,229 3480.9,225.48 3494.7,213.61 3507,202.31", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3663.4,178", + pos="3645.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3702.9,221.5", - pos="e,3659.4,196.06 2388.5,251.7 2419.1,249.86 2450.7,248.19 2480.4,247 2512.5,245.72 3610,245.89 3637.4,229 3646,223.71 3651.8,214.61 \ -3655.8,205.6", + lp="3687.9,221.5", + pos="e,3642.4,196.18 3460.8,253.27 3536.6,247.5 3609,239.41 3623.4,229 3631.1,223.42 3636.1,214.54 3639.4,205.8", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3778.4,178", + width=2.1304]; + "cell line to disease or phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3818.9,221.5", + pos="e,3771.3,195.98 3449.5,252.39 3581.1,243.72 3736.8,232.76 3743.4,229 3753.1,223.5 3760.7,214.1 3766.3,204.93", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3949.4,178", + width=2.1304]; + "cell line to disease or phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3964.9,221.5", + pos="e,3932.9,195.75 3446.3,252.16 3474.8,250.37 3503.9,248.59 3531.4,247 3609.4,242.49 3808.9,255.5 3882.4,229 3898.1,223.32 3913.3,\ +212.6 3925.2,202.54", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4082.4,178", + width=1.0652]; + "cell line to disease or phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="4100.9,221.5", + pos="e,4066.6,194.71 3443.4,251.98 3472.8,250.17 3503,248.43 3531.4,247 3586.1,244.24 3973.4,249.02 4024.4,229 4032.3,225.9 4046.7,213.48 \ +4059.2,201.8", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4178.4,178", + width=1.0652]; + "cell line to disease or phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4220.4,221.5", + pos="e,4176,196.39 3442,251.88 3471.8,250.06 3502.5,248.35 3531.4,247 3566.1,245.38 4128.7,248.67 4157.4,229 4165.2,223.66 4170.1,214.84 \ +4173.2,206.07", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4311.4,178", + width=2.1304]; + "cell line to disease or phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4378.9,221.5", + pos="e,4303.8,196.2 3441.3,251.81 3471.3,249.99 3502.3,248.29 3531.4,247 3572.6,245.17 4237.8,248.03 4274.4,229 4284.6,223.72 4292.7,\ +214.23 4298.7,204.92", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4500.4,178", + width=2.1304]; + "cell line to disease or phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4568.9,221.5", + pos="e,4495.1,196.12 3440.2,251.75 3470.6,249.92 3501.9,248.23 3531.4,247 3557.5,245.91 4447.8,242.07 4470.4,229 4479.5,223.73 4486.2,\ +214.5 4490.8,205.39", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4690.4,178", + width=1.0652]; + "cell line to disease or phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4740.4,221.5", + pos="e,4683.7,196.2 3439.5,251.71 3470.1,249.87 3501.7,248.19 3531.4,247 3562.6,245.75 4628.9,243.84 4656.4,229 4666.1,223.77 4673.6,\ +214.41 4679,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4849.4,178", + width=1.0652]; + "cell line to disease or phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4893.4,221.5", + pos="e,4842,195.75 3439.2,251.68 3469.9,249.84 3501.6,248.17 3531.4,247 3567,245.61 4780.7,245.24 4812.4,229 4822.7,223.7 4830.9,214.02 \ +4836.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="5000.4,178", + width=1.0652]; + "cell line to disease or phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5053.4,221.5", + pos="e,4992.4,195.78 3438.8,251.67 3469.6,249.82 3501.4,248.15 3531.4,247 3571.1,245.47 4925.8,246.65 4961.4,229 4972.1,223.68 4980.8,\ +213.86 4987.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5171.4,178", + width=1.0652]; + "cell line to disease or phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5219.9,221.5", + pos="e,5163.1,195.8 3438.5,251.66 3469.4,249.8 3501.3,248.14 3531.4,247 3575.8,245.32 5091.4,248.48 5131.4,229 5142.3,223.7 5151.1,213.89 \ +5157.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5333.4,178", + width=2.347]; + "cell line to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5381.9,221.5", + pos="e,5324.8,196.3 3438.5,251.63 3469.4,249.78 3501.3,248.12 3531.4,247 3580.3,245.18 5249.4,250.43 5293.4,229 5304.1,223.78 5312.9,\ +214.17 5319.4,204.76", style=solid]; type [height=0.5, - pos="3751.4,178", + pos="5467.4,178", width=0.86659]; "cell line to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="3780.4,221.5", - pos="e,3759.9,195.59 2388.2,251.68 2418.9,249.84 2450.6,248.17 2480.4,247 2498.1,246.3 3745.9,241.64 3758.4,229 3764.5,222.81 3764.8,\ -213.91 3762.9,205.33", + lp="5481.4,221.5", + pos="e,5468.2,196.19 3438.1,251.63 3469.1,249.77 3501.2,248.11 3531.4,247 3558.1,246.02 5434.5,245.64 5455.4,229 5462.2,223.55 5465.6,\ +214.93 5467.2,206.37", style=solid]; category [height=0.5, - pos="3852.4,178", + pos="5568.4,178", width=1.4263]; "cell line to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="3853.9,221.5", - pos="e,3840.4,195.9 2388.2,251.67 2418.9,249.83 2450.6,248.16 2480.4,247 2517,245.57 3766.5,242.93 3800.4,229 3813.4,223.67 3825,213.43 \ -3833.9,203.59", + lp="5560.9,221.5", + pos="e,5552.8,195.26 3438.1,251.63 3469.1,249.77 3501.2,248.11 3531.4,247 3586.1,244.99 5449.5,246.48 5501.4,229 5517.6,223.54 5533.1,\ +212.51 5545.1,202.2", style=solid]; subject [height=0.5, - pos="3966.4,178", + pos="5682.4,178", width=1.2277]; "cell line to disease or phenotypic feature association" -> subject [color=blue, label=subject, - lp="3946.4,221.5", - pos="e,3948.9,194.53 2387.8,251.67 2418.6,249.83 2450.4,248.15 2480.4,247 2558.6,243.98 3814.5,251.71 3889.4,229 3908.1,223.33 3926.5,\ -211.63 3940.7,200.97", + lp="5657.4,221.5", + pos="e,5662.9,194.34 3438.1,251.61 3469.1,249.76 3501.2,248.1 3531.4,247 3588.7,244.91 5541.1,244.17 5596.4,229 5617.3,223.26 5638.4,\ +211.1 5654.5,200.21", style=solid]; relation [height=0.5, - pos="3917.4,18", + pos="5633.4,18", width=1.2999]; - object -> relation [pos="e,3905.9,35.705 3880,73.174 3886,64.509 3893.4,53.768 3900,44.141", + object -> relation [pos="e,5621.9,35.705 5596,73.174 5602,64.509 5609.4,53.768 5616,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="2527.4,265", + pos="3578.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2658.4,265", + pos="3709.4,265", width=2.0762]; subject -> object [label=relation, - lp="3924.4,134.5", - pos="e,3874.8,108.97 3933.9,165.59 3921.1,159.94 3907,152.13 3896.4,142 3889.4,135.31 3883.7,126.48 3879.3,118.1"]; - subject -> relation [pos="e,3928.6,35.828 3965,159.99 3962.9,139.02 3958,102.55 3947.4,73 3943.9,63.258 3938.8,53.189 3933.8,44.423", + lp="5640.4,134.5", + pos="e,5590.8,108.97 5649.9,165.59 5637.1,159.94 5623,152.13 5612.4,142 5605.4,135.31 5599.7,126.48 5595.3,118.1"]; + subject -> relation [pos="e,5644.6,35.828 5681,159.99 5678.9,139.02 5674,102.55 5663.4,73 5659.9,63.258 5654.8,53.189 5649.8,44.423", style=dotted]; "cell line to disease or phenotypic feature association_subject" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="2900.4,265", + pos="3951.4,265", width=4.1344]; } diff --git a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg index d092c18974..7263c591ec 100644 --- a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + cell line to disease or phenotypic feature association - -cell line to disease or phenotypic feature association + +cell line to disease or phenotypic feature association @@ -24,7 +24,7 @@ cell line to disease or phenotypic feature association->association - + is_a @@ -37,7 +37,7 @@ cell line to disease or phenotypic feature association->cell line to entity association mixin - + uses @@ -50,8 +50,8 @@ cell line to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - + + uses @@ -63,7 +63,7 @@ cell line to disease or phenotypic feature association->id - + id @@ -76,9 +76,9 @@ cell line to disease or phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ cell line to disease or phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ cell line to disease or phenotypic feature association->description - - -description + + +description @@ -115,8 +115,8 @@ cell line to disease or phenotypic feature association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ cell line to disease or phenotypic feature association->predicate - - + + predicate object - -named thing + +named thing cell line to disease or phenotypic feature association->object - - + + object @@ -154,9 +154,9 @@ cell line to disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ cell line to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ cell line to disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ cell line to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ cell line to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ cell line to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ cell line to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ cell line to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -258,9 +258,9 @@ cell line to disease or phenotypic feature association->original subject - - -original subject + + +original subject @@ -271,104 +271,247 @@ cell line to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string cell line to disease or phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +cell line to disease or phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +cell line to disease or phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +cell line to disease or phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +cell line to disease or phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +cell line to disease or phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +cell line to disease or phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +cell line to disease or phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +cell line to disease or phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +cell line to disease or phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +cell line to disease or phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +cell line to disease or phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + cell line to disease or phenotypic feature association->type - - -type + + +type - + category - -category + +category - + cell line to disease or phenotypic feature association->category - - -category + + +category - + subject - -subject + +subject - + cell line to disease or phenotypic feature association->subject - - -subject + + +subject - + relation - -relation + +relation - + object->relation - - + + - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + subject->relation - - + + - + cell line to disease or phenotypic feature association_subject - -disease or phenotypic feature + +disease or phenotypic feature diff --git a/graphviz/chemical_affects_gene_association.gv b/graphviz/chemical_affects_gene_association.gv index ac7030ef05..ffb6f73a80 100644 --- a/graphviz/chemical_affects_gene_association.gv +++ b/graphviz/chemical_affects_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,8928.6,283"]; + graph [bb="0,0,9821.6,283"]; node [label="\N"]; "chemical affects gene association" [height=0.5, label="chemical affects gene association", - pos="2699.4,265", + pos="3592.4,265", width=4.5857]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical affects gene association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.81 2534.5,263.79 2023.9,262.82 489.39,257.56 266.39,229 213.1,222.17 153.57,206.64 112.64,194.69"]; + pos="e,102.9,191.86 3427.9,263.32 2779,260.5 424.35,248.92 266.39,229 213.09,222.28 153.56,206.73 112.63,194.74"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "chemical affects gene association" -> id [color=blue, label=id, lp="396.39,221.5", - pos="e,210.38,189.98 2534.7,263.3 2042,260.95 600.39,252.15 389.39,229 317.22,221.08 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ + pos="e,210.38,189.98 3427.4,264.06 2814.9,264.02 691.69,261.52 389.39,229 317.2,221.23 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ 219.89,193.15", style=solid]; iri [color=blue, @@ -30,7 +30,7 @@ digraph { "chemical affects gene association" -> iri [color=blue, label=iri, lp="509.39,221.5", - pos="e,315.3,190.2 2535.1,263.09 2059.3,260.23 701.17,250.27 501.39,229 426.6,221.04 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ + pos="e,315.3,190.2 3427.5,263.92 2829.2,263.38 792.3,259.3 501.39,229 426.58,221.21 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ 325.06,193.15", style=solid]; name [color=blue, @@ -41,7 +41,7 @@ digraph { "chemical affects gene association" -> name [color=blue, label=name, lp="616.39,221.5", - pos="e,438.99,191.45 2534.8,263.47 2072.9,261.69 785.88,254.46 596.39,229 545.09,222.11 487.88,206.45 448.77,194.49", + pos="e,438.98,191.51 3427.3,264.37 2840.5,265.38 876.61,265.94 596.39,229 545.08,222.24 487.87,206.56 448.76,194.55", style=solid]; description [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { "chemical affects gene association" -> description [color=blue, label=description, lp="736.89,221.5", - pos="e,585.45,194.17 2534.1,264.09 2086.9,263.9 874.6,260.47 696.39,229 661.33,222.81 623.33,209.44 595.03,198.08", + pos="e,585.15,194.1 3427.8,263.46 2834.2,261.34 831.31,252.45 696.39,229 661.19,222.88 623.06,209.44 594.73,198.03", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,7 +61,7 @@ digraph { "chemical affects gene association" -> "has attribute" [color=blue, label="has attribute", lp="882.39,221.5", - pos="e,725.97,192.85 2534.5,263.97 2109.8,263.46 999.58,259.22 835.39,229 800.42,222.56 762.56,208.43 735.19,196.83", + pos="e,725.96,192.9 3427.8,263.42 2853.1,261.18 963.09,252.1 835.39,229 800.4,222.67 762.54,208.53 735.18,196.9", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical affects gene association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.49 2535.8,262.56 2141.1,258.8 1157.8,247.69 1009.4,229 956.08,222.28 896.46,205.73 857.14,193.5", + lp="1037.4,221.5", + pos="e,847.4,190.57 3427.2,263.85 2895.1,263.09 1246.8,258.36 1008.4,229 955.42,222.48 896.26,205.95 857.14,193.67", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical affects gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.67,193.12 2535.7,262.48 2164.4,258.71 1279.9,247.86 1145.4,229 1097.6,222.29 1044.5,207.82 1006.5,196.17", + lp="1177.9,221.5", + pos="e,996.43,193.22 3427.4,263.96 2914.4,263.52 1368.6,259.64 1144.4,229 1096.8,222.49 1044,208 1006.2,196.29", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical affects gene association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1147.8,192.64 2536,262.35 2189.5,258.5 1403.1,247.81 1282.4,229 1239.1,222.26 1191.4,207.69 1157.4,196.01", + lp="1325.4,221.5", + pos="e,1147.6,192.75 3427.5,264.08 2934.3,263.96 1491.3,260.86 1281.4,229 1238.3,222.47 1190.9,207.88 1157.1,196.13", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "chemical affects gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1487.9,221.5", - pos="e,1306.8,193.43 2534.3,264.56 2242.5,264.69 1646.9,260.86 1441.4,229 1398.4,222.34 1351.1,208.27 1316.6,196.75", + lp="1486.9,221.5", + pos="e,1306.2,193.44 3427.3,263.83 2957.4,263 1634.3,258.08 1440.4,229 1397.5,222.57 1350.2,208.41 1316,196.8", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "chemical affects gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1647.9,221.5", - pos="e,1498.3,195.4 2536.1,262.31 2248.6,258.82 1673.5,249.38 1583.4,229 1557,223.02 1529.1,210.9 1507.5,200.09", + lp="1645.9,221.5", + pos="e,1497.8,195.52 3428.4,262.93 2964.5,259.68 1670.8,248.86 1581.4,229 1555.3,223.21 1527.9,211.09 1506.7,200.23", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "chemical affects gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1823.4,221.5", - pos="e,1707.9,196.44 2535.7,262.48 2267.7,259.38 1761.5,250.67 1728.4,229 1720.3,223.71 1714.9,214.9 1711.3,206.13", + lp="1821.4,221.5", + pos="e,1707.2,196.45 3427.9,263.25 2978.7,260.91 1761.6,252.42 1726.4,229 1718.5,223.73 1713.4,214.92 1710.1,206.15", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "chemical affects gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2032.9,221.5", - pos="e,1927.7,196.32 2535.9,262.28 2315.3,259.15 1947.1,250.68 1926.4,229 1920.4,222.69 1920.8,213.94 1923.7,205.53", + lp="2030.9,221.5", + pos="e,1926.6,196.33 3427.8,263.56 3012.1,262.06 1950.5,255.61 1924.4,229 1918.2,222.7 1918.9,213.95 1922.1,205.54", style=solid]; timepoint [color=blue, height=0.5, @@ -140,8 +140,8 @@ digraph { width=1.5346]; "chemical affects gene association" -> timepoint [color=blue, label=timepoint, - lp="2194.4,221.5", - pos="e,2129.4,196.05 2539.7,260.34 2392.6,255.89 2192.3,246.67 2159.4,229 2149.2,223.53 2140.9,214 2134.7,204.73", + lp="2192.4,221.5", + pos="e,2128.7,196.19 3427.4,263.89 3062.1,263.11 2212.6,258.16 2157.4,229 2147.4,223.7 2139.5,214.21 2133.6,204.91", style=solid]; "original subject" [color=blue, height=0.5, @@ -150,8 +150,8 @@ digraph { width=1.0652]; "chemical affects gene association" -> "original subject" [color=blue, label="original subject", - lp="2297.4,221.5", - pos="e,2231.2,196.32 2537.7,261.31 2414.8,257.68 2263.2,249.12 2241.4,229 2235.2,223.31 2232.5,214.89 2231.6,206.58", + lp="2294.4,221.5", + pos="e,2229.9,196.34 3428.8,262.57 3073.2,259.1 2259.9,248.99 2238.4,229 2232.3,223.32 2230,214.91 2229.6,206.6", style=solid]; "original predicate" [color=blue, height=0.5, @@ -160,8 +160,8 @@ digraph { width=1.5887]; "chemical affects gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2431.9,221.5", - pos="e,2350,196.14 2536.2,262.06 2466.7,258.17 2395.5,249.12 2368.4,229 2360.8,223.37 2356,214.48 2352.8,205.75", + lp="2427.9,221.5", + pos="e,2348.4,196.29 3427.3,264.25 3102.2,264.05 2406.4,259.99 2364.4,229 2357.1,223.6 2352.9,214.88 2350.5,206.22", style=solid]; "original object" [color=blue, height=0.5, @@ -170,294 +170,410 @@ digraph { width=1.0652]; "chemical affects gene association" -> "original object" [color=blue, label="original object", - lp="2566.9,221.5", - pos="e,2477.4,194.64 2583.3,252.1 2560,246.93 2536.3,239.55 2515.4,229 2511.7,227.11 2497.6,214.02 2484.7,201.7", + lp="2571.9,221.5", + pos="e,2475,195.34 3427.1,264.56 3147.3,264.64 2602.5,260.63 2520.4,229 2505.9,223.41 2492.4,212.63 2482,202.51", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "chemical affects gene association" -> "subject category" [color=blue, + label="subject category", + lp="2708.9,221.5", + pos="e,2607.3,195.8 3427.4,264.01 3176.1,263.1 2719.2,257.48 2649.4,229 2636,223.54 2623.8,213.28 2614.3,203.47", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "chemical affects gene association" -> "object category" [color=blue, + label="object category", + lp="2837.9,221.5", + pos="e,2766.4,196.24 3430.2,261.65 3201.2,257.66 2807.8,248.07 2782.4,229 2775.1,223.55 2770.9,214.81 2768.5,206.16", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "chemical affects gene association" -> "subject closure" [color=blue, + label="subject closure", + lp="2958.9,221.5", + pos="e,2895.4,196.31 3431.3,260.98 3234,256.53 2923.4,246.74 2904.4,229 2898.3,223.29 2895.9,214.88 2895.3,206.57", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2997.4,178", + width=1.0652]; + "chemical affects gene association" -> "object closure" [color=blue, + label="object closure", + lp="3083.4,221.5", + pos="e,3004.8,196.03 3431.3,260.9 3278.6,256.83 3067.5,247.86 3033.4,229 3023.6,223.57 3015.7,214.18 3009.9,205", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3130.4,178", + width=2.1304]; + "chemical affects gene association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3234.9,221.5", + pos="e,3131.5,196.13 3433.7,259.96 3315.2,255.55 3170,246.6 3147.4,229 3140.2,223.42 3136,214.66 3133.6,206.02", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "chemical affects gene association" -> "object category closure" [color=blue, + label="object category closure", + lp="3418.9,221.5", + pos="e,3322.9,196.29 3441.3,257.71 3395.2,252.79 3352.1,244.14 3335.4,229 3329,223.21 3325.7,214.66 3324.1,206.26", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "chemical affects gene association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3578.4,221.5", + pos="e,3507.5,196.09 3532,248.19 3523.5,243.39 3515.8,237.14 3510.4,229 3506,222.34 3505.1,214.03 3505.8,206.11", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3619.4,178", + width=1.0652]; + "chemical affects gene association" -> "object namespace" [color=blue, + label="object namespace", + lp="3717.4,221.5", + pos="e,3638.4,194.12 3632.5,247.38 3639.6,242.53 3646.2,236.48 3650.4,229 3655.5,219.97 3651.7,210.23 3645.2,201.78", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3714.4,178", + width=1.0652]; + "chemical affects gene association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3862.4,221.5", + pos="e,3743.7,189.79 3719.7,253.51 3749.7,248.32 3775.7,240.57 3785.4,229 3789.7,223.88 3788.9,219.66 3785.4,214 3781.4,207.54 3767.5,\ +200.12 3753.1,193.78", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3809.4,178", + width=1.0652]; + "chemical affects gene association" -> "object label closure" [color=blue, + label="object label closure", + lp="4025.9,221.5", + pos="e,3838.4,189.94 3710.5,252.35 3811.2,242.38 3939.9,229.55 3940.4,229 3982.9,181.95 3981.1,231.18 3857.4,196 3854.3,195.12 3851.1,\ +194.14 3847.9,193.12", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="3950.4,178", + width=2.347]; + "chemical affects gene association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4172.9,221.5", + pos="e,4013.4,190.03 3707.5,252.05 3727.1,250.21 3747.3,248.45 3766.4,247 3784.9,245.6 4086.7,242.45 4099.4,229 4104,224.16 4103.5,219.23 \ +4099.4,214 4094.2,207.48 4058.5,198.96 4023.3,191.96", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4084.4,178", width=0.86659]; "chemical affects gene association" -> type [color=blue, label=type, - lp="2657.4,221.5", - pos="e,2574.1,189.21 2670,247.25 2660.7,241.68 2650.5,235.29 2641.4,229 2632.5,222.88 2631.5,219.69 2622.4,214 2610.1,206.35 2596,199.2 \ -2583.4,193.39", + lp="4266.4,221.5", + pos="e,4107.9,189.9 3706,251.91 3726.1,250.05 3746.9,248.32 3766.4,247 3793,245.2 4227.9,248.22 4246.4,229 4251,224.2 4250.7,219.05 4246.4,\ +214 4228.6,193.41 4151.6,203.26 4125.4,196 4122.8,195.27 4120.1,194.42 4117.4,193.5", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4185.4,178", width=1.4263]; "chemical affects gene association" -> category [color=blue, label=category, - lp="2716.9,221.5", - pos="e,2664.4,195.5 2693,246.83 2689.1,236.94 2683.6,224.44 2677.4,214 2675.3,210.54 2673,207.02 2670.6,203.62", + lp="4321.9,221.5", + pos="e,4224,190.03 3706,251.86 3726.1,250.01 3746.9,248.29 3766.4,247 3795.2,245.09 4266.3,249.79 4286.4,229 4291,224.21 4290.3,219.43 \ +4286.4,214 4283,209.18 4257.9,200.47 4233.6,192.95", style=solid]; "subject form or variant qualifier" [height=0.5, - pos="2879.4,178", + pos="4414.4,178", width=4.4232]; "chemical affects gene association" -> "subject form or variant qualifier" [color=blue, label="subject form or variant qualifier", - lp="2914.9,221.5", - pos="e,2844,195.69 2734.5,247.41 2763.2,233.88 2803.8,214.69 2834.8,200.07", + lp="4496.9,221.5", + pos="e,4400.5,196.33 3705.6,251.84 3725.8,249.98 3746.7,248.26 3766.4,247 3832,242.8 4296.3,253.08 4357.4,229 4371.1,223.62 4383.6,213.43 \ +4393.5,203.65", style=solid]; "subject part qualifier" [height=0.5, - pos="3165.4,178", + pos="4700.4,178", width=3.015]; "chemical affects gene association" -> "subject part qualifier" [color=blue, label="subject part qualifier", - lp="3157.9,221.5", - pos="e,3130.3,195.13 2817.4,252.36 2909.2,243.19 3022.7,231.54 3033.4,229 3063.4,221.87 3095.8,209.66 3121,199.09", + lp="4725.9,221.5", + pos="e,4679.1,195.72 3704.6,251.77 3725.1,249.89 3746.4,248.19 3766.4,247 3860.6,241.41 4524.6,254.75 4615.4,229 4635.1,223.41 4654.9,\ +212.14 4670.5,201.71", style=solid]; "subject derivative qualifier" [height=0.5, - pos="3427.4,178", + pos="4962.4,178", width=3.7733]; "chemical affects gene association" -> "subject derivative qualifier" [color=blue, label="subject derivative qualifier", - lp="3402.9,221.5", - pos="e,3378.4,194.91 2814,252.02 2833.8,250.17 2854.2,248.41 2873.4,247 3034.9,235.12 3077.3,253.74 3237.4,229 3282.1,222.09 3331.5,208.92 \ -3368.7,197.82", + lp="4963.9,221.5", + pos="e,4922.5,195.26 3704.1,251.75 3724.8,249.86 3746.2,248.16 3766.4,247 3881.7,240.38 4691.5,247.72 4805.4,229 4842.3,222.93 4882.5,\ +210.01 4913,198.82", style=solid]; "subject aspect qualifier" [height=0.5, - pos="3700.4,178", + pos="5235.4,178", width=3.3039]; "chemical affects gene association" -> "subject aspect qualifier" [color=blue, label="subject aspect qualifier", - lp="3663.9,221.5", - pos="e,3652,194.46 2812.6,251.8 2832.8,249.95 2853.7,248.24 2873.4,247 3013.2,238.19 3364.7,248.34 3503.4,229 3550.7,222.4 3603.1,208.8 \ -3641.9,197.44", + lp="5214.9,221.5", + pos="e,5192.9,194.92 3704.1,251.69 3724.8,249.81 3746.2,248.12 3766.4,247 3910.4,238.98 4921.8,250.44 5064.4,229 5105.2,222.87 5149.9,\ +209.56 5183.3,198.22", style=solid]; "subject context qualifier" [height=0.5, - pos="3960.4,178", + pos="5495.4,178", width=3.4303]; "chemical affects gene association" -> "subject context qualifier" [color=blue, label="subject context qualifier", - lp="3920.4,221.5", - pos="e,3909.4,194.43 2811.6,251.76 2832.1,249.88 2853.4,248.18 2873.4,247 3068.2,235.5 3557.8,253.85 3751.4,229 3802.1,222.49 3858.4,\ -208.63 3899.8,197.15", + lp="5465.4,221.5", + pos="e,5448,194.69 3703.7,251.7 3724.5,249.8 3746.1,248.11 3766.4,247 3936.8,237.69 5133.2,251.57 5302.4,229 5348.8,222.8 5400.2,209.17 \ +5438.2,197.71", style=solid]; "subject direction qualifier" [height=0.5, - pos="4231.4,178", + pos="5766.4,178", width=3.6108]; "chemical affects gene association" -> "subject direction qualifier" [color=blue, label="subject direction qualifier", - lp="4189.4,221.5", - pos="e,4177.7,194.49 2811.1,251.72 2831.8,249.84 2853.2,248.14 2873.4,247 3125.9,232.69 3760.3,259.19 4011.4,229 4064.8,222.58 4124.2,\ -208.66 4167.8,197.14", + lp="5730.4,221.5", + pos="e,5715.2,194.59 3703.7,251.67 3724.5,249.78 3746.1,248.09 3766.4,247 3965,236.32 5359,253.19 5556.4,229 5607.4,222.76 5663.9,208.87 \ +5705.5,197.32", style=solid]; "object form or variant qualifier" [height=0.5, - pos="4533.4,178", + pos="6068.4,178", width=4.2788]; "chemical affects gene association" -> "object form or variant qualifier" [color=blue, label="object form or variant qualifier", - lp="4492.9,221.5", - pos="e,4472.5,194.58 2811.1,251.67 2831.8,249.79 2853.2,248.11 2873.4,247 3186.7,229.73 3973.3,262.15 4285.4,229 4345.8,222.59 4413.2,\ -208.52 4462.6,196.94", + lp="6030.9,221.5", + pos="e,6008.7,194.72 3703.7,251.65 3724.5,249.76 3746.1,248.08 3766.4,247 3995,234.86 5598.8,253.27 5826.4,229 5885.1,222.74 5950.7,208.74 \ +5998.8,197.15", style=solid]; "object part qualifier" [height=0.5, - pos="4808.4,178", + pos="6343.4,178", width=2.8525]; "chemical affects gene association" -> "object part qualifier" [color=blue, label="object part qualifier", - lp="4757.4,221.5", - pos="e,4761.1,194.1 2810.7,251.67 2831.5,249.78 2853.1,248.1 2873.4,247 3065.8,236.62 4416.3,253.42 4607.4,229 4656.7,222.7 4711.4,208.61 \ -4751.3,197", + lp="6294.4,221.5", + pos="e,6296.8,194.14 3703.7,251.63 3724.5,249.74 3746.1,248.07 3766.4,247 4030.4,233.13 5883.2,262.6 6145.4,229 6194,222.77 6247.9,208.68 \ +6287.1,197.04", style=solid]; "object aspect qualifier" [height=0.5, - pos="5042.4,178", + pos="6577.4,178", width=3.1594]; "chemical affects gene association" -> "object aspect qualifier" [color=blue, label="object aspect qualifier", - lp="4993.9,221.5", - pos="e,4992.5,194.24 2810.7,251.66 2831.5,249.76 2853.1,248.08 2873.4,247 3090.8,235.41 4616.3,255.38 4832.4,229 4883.9,222.72 4941.1,\ -208.61 4982.8,196.98", + lp="6529.9,221.5", + pos="e,6528,194.27 3703.7,251.62 3724.5,249.73 3746.1,248.06 3766.4,247 4055.2,231.92 6082.3,264.03 6369.4,229 6420.4,222.77 6477.1,208.67 \ +6518.3,197.02", style=solid]; "object context qualifier" [height=0.5, - pos="5292.4,178", + pos="6827.4,178", width=3.2858]; "chemical affects gene association" -> "object context qualifier" [color=blue, label="object context qualifier", - lp="5244.4,221.5", - pos="e,5241.3,194.25 2810.7,251.64 2831.5,249.75 2853.1,248.07 2873.4,247 3118,234.08 4834.2,257.91 5077.4,229 5130.2,222.73 5188.9,208.57 \ -5231.6,196.92", + lp="6780.4,221.5", + pos="e,6776.5,194.28 3703.2,251.65 3724.2,249.75 3745.9,248.06 3766.4,247 4082.3,230.6 6299.3,266.22 6613.4,229 6665.8,222.79 6724.1,\ +208.68 6766.6,197.03", style=solid]; "causal mechanism qualifier" [height=0.5, - pos="5565.4,178", + pos="7100.4,178", width=3.8094]; "chemical affects gene association" -> "causal mechanism qualifier" [color=blue, label="causal mechanism qualifier", - lp="5519.9,221.5", - pos="e,5508.7,194.5 2810.7,251.62 2831.5,249.74 2853.1,248.06 2873.4,247 3146.1,232.71 5059.9,258.69 5331.4,229 5388.5,222.75 5452.2,\ -208.65 5498.8,197.02", + lp="7055.9,221.5", + pos="e,7044,194.52 3703.2,251.64 3724.2,249.74 3745.9,248.06 3766.4,247 4110.5,229.23 6524.9,266.34 6867.4,229 6924.3,222.8 6987.7,208.7 \ +7034,197.04", style=solid]; "anatomical context qualifier" [height=0.5, - pos="5861.4,178", + pos="7396.4,178", width=3.8997]; "chemical affects gene association" -> "anatomical context qualifier" [color=blue, label="anatomical context qualifier", - lp="5815.4,221.5", - pos="e,5803.2,194.51 2810.2,251.65 2831.2,249.75 2852.9,248.06 2873.4,247 3178.3,231.14 5317.8,261.3 5621.4,229 5680.1,222.76 5745.6,\ -208.61 5793.3,196.96", + lp="7350.4,221.5", + pos="e,7338.5,194.53 3703.2,251.63 3724.2,249.73 3745.9,248.05 3766.4,247 3954.5,237.33 6970.1,248.89 7157.4,229 7215.8,222.8 7281.1,\ +208.65 7328.6,196.98", style=solid]; "qualified predicate" [height=0.5, - pos="6117.4,178", + pos="7652.4,178", width=2.7081]; "chemical affects gene association" -> "qualified predicate" [color=blue, label="qualified predicate", - lp="6064.4,221.5", - pos="e,6071.6,193.92 2810.2,251.64 2831.2,249.74 2852.9,248.06 2873.4,247 3042.4,238.26 5751.5,250.37 5919.4,229 5968.4,222.77 6022.6,\ -208.53 6061.9,196.83", + lp="7599.4,221.5", + pos="e,7606.6,193.94 3703.2,251.63 3724.2,249.72 3745.9,248.05 3766.4,247 3971,236.53 7251.1,254.77 7454.4,229 7503.4,222.79 7557.6,208.55 \ +7596.9,196.85", style=solid]; subject [height=0.5, - pos="6277.4,178", + pos="7812.4,178", width=1.2277]; "chemical affects gene association" -> subject [color=blue, label=subject, - lp="6217.4,221.5", - pos="e,6249.3,192.03 2810.2,251.64 2831.2,249.73 2852.9,248.05 2873.4,247 3054.4,237.68 5956.8,260.02 6135.4,229 6172,222.64 6211.8,207.91 \ -6239.9,196.08", + lp="7752.4,221.5", + pos="e,7784.3,192.04 3703.2,251.62 3724.2,249.72 3745.9,248.04 3766.4,247 3874.7,241.47 7563.5,247.52 7670.4,229 7707,222.65 7746.8,207.92 \ +7774.9,196.09", style=solid]; predicate [height=0.5, - pos="6394.4,178", + pos="7929.4,178", width=1.5165]; "chemical affects gene association" -> predicate [color=blue, label=predicate, - lp="6339.4,221.5", - pos="e,6363.3,192.85 2810.2,251.63 2831.2,249.73 2852.9,248.05 2873.4,247 3060.6,237.38 6062.5,260.08 6247.4,229 6284.5,222.75 6324.9,\ -208.43 6353.9,196.71", + lp="7874.4,221.5", + pos="e,7898.3,192.86 3703.2,251.62 3724.2,249.72 3745.9,248.04 3766.4,247 3877.8,241.32 7672.4,247.45 7782.4,229 7819.5,222.77 7859.9,\ +208.45 7888.9,196.72", style=solid]; object [height=0.5, - pos="6344.4,91", + pos="7879.4,91", width=1.0832]; "chemical affects gene association" -> object [color=blue, label=object, - lp="6487.4,178", - pos="e,6373.9,102.76 2810.2,251.63 2831.2,249.73 2852.9,248.05 2873.4,247 2970.6,242.01 6281.9,247.96 6377.4,229 6415.5,221.43 6436.7,\ -228.26 6458.4,196 6483.8,158.28 6425.4,124.88 6383.2,106.64", + lp="8022.4,178", + pos="e,7908.9,102.76 3703.2,251.62 3724.2,249.72 3745.9,248.04 3766.4,247 3881.4,241.14 7799.4,251.38 7912.4,229 7950.5,221.44 7971.7,\ +228.26 7993.4,196 8018.8,158.28 7960.4,124.88 7918.2,106.64", style=solid]; "object direction qualifier" [height=0.5, - pos="6672.4,178", + pos="8207.4,178", width=3.4664]; "chemical affects gene association" -> "object direction qualifier" [color=blue, label="object direction qualifier", - lp="6655.4,221.5", - pos="e,6629.4,195.03 2810.2,251.63 2831.2,249.73 2852.9,248.05 2873.4,247 3074.6,236.69 6300,257.74 6499.4,229 6540.7,223.05 6585.9,209.74 \ -6619.7,198.34", + lp="8190.4,221.5", + pos="e,8164.8,194.92 3703.2,251.61 3724.2,249.71 3745.9,248.04 3766.4,247 4003.2,234.96 7799.7,262.74 8034.4,229 8075.8,223.05 8121.2,\ +209.66 8155.1,198.23", style=solid]; "species context qualifier" [height=0.5, - pos="6939.4,178", + pos="8474.4,178", width=3.4483]; "chemical affects gene association" -> "species context qualifier" [color=blue, label="species context qualifier", - lp="6908.9,221.5", - pos="e,6892.3,194.79 2810.2,251.62 2831.2,249.72 2852.9,248.04 2873.4,247 3088.3,236.02 6534,256.84 6747.4,229 6793.6,222.97 6844.7,209.33 \ -6882.5,197.82", + lp="8443.9,221.5", + pos="e,8427.3,194.8 3703.2,251.61 3724.2,249.71 3745.9,248.04 3766.4,247 4017,234.29 8033.6,261.37 8282.4,229 8328.6,222.98 8379.7,209.34 \ +8417.5,197.83", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2920.4,265", + pos="3813.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3051.4,265", + pos="3944.4,265", width=2.0762]; "chemical affects gene association_subject form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="3402.4,265", + pos="4295.4,265", width=7.1855]; "chemical affects gene association_subject part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="3927.4,265", + pos="4820.4,265", width=6.8966]; "chemical affects gene association_subject derivative qualifier" [color=blue, height=0.5, label=ChemicalEntityDerivativeEnum, - pos="4351.4,265", + pos="5244.4,265", width=4.3871]; "chemical affects gene association_subject aspect qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="4775.4,265", + pos="5668.4,265", width=6.8966]; "chemical affects gene association_subject context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="5133.4,265", + pos="6026.4,265", width=2.5456]; "chemical affects gene association_subject direction qualifier" [color=blue, height=0.5, label=DirectionQualifierEnum, - pos="5364.4,265", + pos="6257.4,265", width=3.358]; "chemical affects gene association_object form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="5762.4,265", + pos="6655.4,265", width=7.1855]; "chemical affects gene association_object part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="6287.4,265", + pos="7180.4,265", width=6.8966]; "chemical affects gene association_object aspect qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="6802.4,265", + pos="7695.4,265", width=6.8966]; "chemical affects gene association_object context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="7160.4,265", + pos="8053.4,265", width=2.5456]; "chemical affects gene association_causal mechanism qualifier" [color=blue, height=0.5, label=CausalMechanismQualifierEnum, - pos="7432.4,265", + pos="8325.4,265", width=4.5135]; "chemical affects gene association_anatomical context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="7704.4,265", + pos="8597.4,265", width=2.5456]; "chemical affects gene association_qualified predicate" [color=blue, height=0.5, label=string, - pos="7852.4,265", + pos="8745.4,265", width=1.0652]; subject -> object [label=relation, - lp="6343.4,134.5", - pos="e,6331.7,108.05 6290.3,160.61 6300.3,147.95 6314.3,130.24 6325.5,115.98"]; + lp="7878.4,134.5", + pos="e,7866.7,108.05 7825.3,160.61 7835.3,147.95 7849.3,130.24 7860.5,115.98"]; relation [height=0.5, - pos="6289.4,18", + pos="7824.4,18", width=1.2999]; - subject -> relation [pos="e,6288.1,36.188 6278.7,159.79 6280.8,132.48 6284.8,78.994 6287.3,46.38", + subject -> relation [pos="e,7823.1,36.188 7813.7,159.79 7815.8,132.48 7819.8,78.994 7822.3,46.38", style=dotted]; "chemical affects gene association_subject" [color=blue, height=0.5, label="chemical entity", - pos="7990.4,265", + pos="8883.4,265", width=2.2748]; "chemical affects gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="8168.4,265", + pos="9061.4,265", width=2.1665]; - object -> relation [pos="e,6302.2,35.54 6331.9,73.889 6325,64.939 6316.2,53.617 6308.4,43.584", + object -> relation [pos="e,7837.2,35.54 7866.9,73.889 7860,64.939 7851.2,53.617 7843.4,43.584", style=dotted]; "chemical affects gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="8374.4,265", + pos="9267.4,265", width=3.0692]; "chemical affects gene association_object direction qualifier" [color=blue, height=0.5, label=DirectionQualifierEnum, - pos="8623.4,265", + pos="9516.4,265", width=3.358]; "chemical affects gene association_species context qualifier" [color=blue, height=0.5, label="organism taxon", - pos="8845.4,265", + pos="9738.4,265", width=2.3109]; } diff --git a/graphviz/chemical_affects_gene_association.svg b/graphviz/chemical_affects_gene_association.svg index 02bdbcaf9d..5611c2887b 100644 --- a/graphviz/chemical_affects_gene_association.svg +++ b/graphviz/chemical_affects_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical affects gene association - -chemical affects gene association + +chemical affects gene association @@ -24,8 +24,8 @@ chemical affects gene association->association - - + + is_a @@ -37,7 +37,7 @@ chemical affects gene association->id - + id @@ -50,7 +50,7 @@ chemical affects gene association->iri - + iri @@ -63,8 +63,8 @@ chemical affects gene association->name - - + + name @@ -76,8 +76,8 @@ chemical affects gene association->description - - + + description @@ -89,8 +89,8 @@ chemical affects gene association->has attribute - - + + has attribute @@ -102,9 +102,9 @@ chemical affects gene association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical affects gene association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical affects gene association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ chemical affects gene association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ chemical affects gene association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ chemical affects gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ chemical affects gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ chemical affects gene association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ chemical affects gene association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ chemical affects gene association->original predicate - - -original predicate + + +original predicate @@ -232,414 +232,557 @@ chemical affects gene association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical affects gene association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical affects gene association->object category + + +object category + + + +subject closure + +string + + + +chemical affects gene association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical affects gene association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical affects gene association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical affects gene association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical affects gene association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical affects gene association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical affects gene association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical affects gene association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical affects gene association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical affects gene association->type - - -type + + +type - + category - -category + +category - + chemical affects gene association->category - - -category + + +category - + subject form or variant qualifier - -subject form or variant qualifier + +subject form or variant qualifier - + chemical affects gene association->subject form or variant qualifier - - -subject form or variant qualifier + + +subject form or variant qualifier - + subject part qualifier - -subject part qualifier + +subject part qualifier - + chemical affects gene association->subject part qualifier - - -subject part qualifier + + +subject part qualifier - + subject derivative qualifier - -subject derivative qualifier + +subject derivative qualifier - + chemical affects gene association->subject derivative qualifier - - -subject derivative qualifier + + +subject derivative qualifier - + subject aspect qualifier - -subject aspect qualifier + +subject aspect qualifier - + chemical affects gene association->subject aspect qualifier - - -subject aspect qualifier + + +subject aspect qualifier - + subject context qualifier - -subject context qualifier + +subject context qualifier - + chemical affects gene association->subject context qualifier - - -subject context qualifier + + +subject context qualifier - + subject direction qualifier - -subject direction qualifier + +subject direction qualifier - + chemical affects gene association->subject direction qualifier - - -subject direction qualifier + + +subject direction qualifier - + object form or variant qualifier - -object form or variant qualifier + +object form or variant qualifier - + chemical affects gene association->object form or variant qualifier - - -object form or variant qualifier + + +object form or variant qualifier - + object part qualifier - -object part qualifier + +object part qualifier - + chemical affects gene association->object part qualifier - - -object part qualifier + + +object part qualifier - + object aspect qualifier - -object aspect qualifier + +object aspect qualifier - + chemical affects gene association->object aspect qualifier - - -object aspect qualifier + + +object aspect qualifier - + object context qualifier - -object context qualifier + +object context qualifier - + chemical affects gene association->object context qualifier - - -object context qualifier + + +object context qualifier - + causal mechanism qualifier - -causal mechanism qualifier + +causal mechanism qualifier - + chemical affects gene association->causal mechanism qualifier - - -causal mechanism qualifier + + +causal mechanism qualifier - + anatomical context qualifier - -anatomical context qualifier + +anatomical context qualifier - + chemical affects gene association->anatomical context qualifier - - -anatomical context qualifier + + +anatomical context qualifier - + qualified predicate - -qualified predicate + +qualified predicate - + chemical affects gene association->qualified predicate - - -qualified predicate + + +qualified predicate - + subject - -subject + +subject - + chemical affects gene association->subject - - -subject + + +subject - + predicate - -predicate + +predicate - + chemical affects gene association->predicate - - -predicate + + +predicate - + object - -object + +object - + chemical affects gene association->object - - -object + + +object - + object direction qualifier - -object direction qualifier + +object direction qualifier - + chemical affects gene association->object direction qualifier - - -object direction qualifier + + +object direction qualifier - + species context qualifier - -species context qualifier + +species context qualifier - + chemical affects gene association->species context qualifier - - -species context qualifier + + +species context qualifier - + association_type - -string + +string - + association_category - -category type + +category type - + chemical affects gene association_subject form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum - + chemical affects gene association_subject part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum - + chemical affects gene association_subject derivative qualifier - -ChemicalEntityDerivativeEnum + +ChemicalEntityDerivativeEnum - + chemical affects gene association_subject aspect qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum - + chemical affects gene association_subject context qualifier - -anatomical entity + +anatomical entity - + chemical affects gene association_subject direction qualifier - -DirectionQualifierEnum + +DirectionQualifierEnum - + chemical affects gene association_object form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum - + chemical affects gene association_object part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum - + chemical affects gene association_object aspect qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum - + chemical affects gene association_object context qualifier - -anatomical entity + +anatomical entity - + chemical affects gene association_causal mechanism qualifier - -CausalMechanismQualifierEnum + +CausalMechanismQualifierEnum - + chemical affects gene association_anatomical context qualifier - -anatomical entity + +anatomical entity - + chemical affects gene association_qualified predicate - -string + +string - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + chemical affects gene association_subject - -chemical entity + +chemical entity - + chemical affects gene association_predicate - -predicate type + +predicate type - + object->relation - - + + - + chemical affects gene association_object - -gene or gene product + +gene or gene product - + chemical affects gene association_object direction qualifier - -DirectionQualifierEnum + +DirectionQualifierEnum - + chemical affects gene association_species context qualifier - -organism taxon + +organism taxon diff --git a/graphviz/chemical_entity_assesses_named_thing_association.gv b/graphviz/chemical_entity_assesses_named_thing_association.gv index 028d2f51ff..21abfc1ba7 100644 --- a/graphviz/chemical_entity_assesses_named_thing_association.gv +++ b/graphviz/chemical_entity_assesses_named_thing_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3016,283"]; + graph [bb="0,0,4748,283"]; node [label="\N"]; "chemical entity assesses named thing association" [height=0.5, label="chemical entity assesses named thing association", - pos="1551.4,265", + pos="2468.4,265", width=6.698]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical entity assesses named thing association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1311.1,263.48 996.67,261.76 462.83,254.95 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2228.1,263.23 1697.2,261.07 456.29,253.47 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "chemical entity assesses named thing association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1314.7,261.55 1028.9,257.76 565.24,248.74 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2229.2,262.49 1721.5,258.91 567.62,248.7 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical entity assesses named thing association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1318.7,260.28 1060.9,255.42 661.85,245.54 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2230.2,262.15 1744,258.01 668.7,246.97 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "chemical entity assesses named thing association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1316.9,260.73 1081.7,256.48 735.85,247.32 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2229.2,262.62 1760.6,259.47 753.68,250.29 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "chemical entity assesses named thing association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1314.2,261.65 1104.4,258.2 814.48,249.75 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2228,263.41 1778.5,261.7 842.8,255.02 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "chemical entity assesses named thing association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1319.8,259.92 1147.1,255.51 926.51,246.59 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2228.5,263.13 1807.6,260.98 968.18,253.63 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical entity assesses named thing association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1326.6,258.44 1227.4,253.71 1109.6,245.01 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2227.2,264.23 1875.1,263.53 1237.4,258.1 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical entity assesses named thing association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1347.8,255.31 1277.9,250.17 1199.3,242 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2227.4,264.24 1904.1,263.42 1347.1,257.68 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical entity assesses named thing association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1386,251.84 1341.3,246.65 1293.2,239.32 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2227.5,264.12 1934.7,263 1457.8,256.76 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "chemical entity assesses named thing association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1454.8,248.42 1429.6,243.29 1402.8,236.84 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2228.5,262.99 1971.7,260.65 1581.3,253.07 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "chemical entity assesses named thing association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1505.9,247.23 1497.5,242.42 1489.4,236.41 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2237,259.94 1992.6,254.85 1634.1,244.84 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "chemical entity assesses named thing association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.7,247.07 1591.6,241.44 1602.5,235.06 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2235.7,260.28 2020.8,255.75 1731.9,246.46 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "chemical entity assesses named thing association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1730.7,252.9 1762.8,247.6 1795.6,239.97 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,202.83 \ -1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2250.7,257.2 2098.9,251.35 1921.5,241.83 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,8 +140,8 @@ digraph { width=1.5346]; "chemical entity assesses named thing association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.15 1722.8,252.32 1870.7,242.22 2060.9,229.2 2061.4,229 2069.3,225.82 2084,213.68 2096.8,202.16", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2285.6,253.26 2215.5,247.53 2149,239.47 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -152,9 +150,8 @@ digraph { width=1.0652]; "chemical entity assesses named thing association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1720.1,252.13 1747.3,250.34 1775.1,248.56 1801.4,247 1879.8,242.34 2079.7,253.29 2154.4,229 2166,225.23 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2277.2,254.02 2248.3,248.68 2224.6,240.74 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -163,9 +160,8 @@ digraph { width=1.5887]; "chemical entity assesses named thing association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.48 1717.8,251.96 1745.7,250.15 1774.4,248.42 1801.4,247 1855.6,244.16 2238.9,248.83 2289.4,229 2297.1,225.96 2311.1,\ -213.96 2323.5,202.48", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2375.5,248.38 2356.5,243.27 2340.5,236.85 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -174,88 +170,204 @@ digraph { width=1.0652]; "chemical entity assesses named thing association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.42 1716.4,251.85 1744.7,250.03 1773.9,248.32 1801.4,247 1836.8,245.3 2410,248.79 2439.4,229 2447.3,223.69 2452.4,214.87 \ -2455.6,206.1", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "chemical entity assesses named thing association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2542.3,247.78 2553.3,243.03 2563.7,236.9 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "chemical entity assesses named thing association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2633.8,251.88 2658.8,246.6 2683.8,239.23 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "chemical entity assesses named thing association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.51 2645.7,252.76 2734.2,246.21 2826.5,237.56 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "chemical entity assesses named thing association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2996.9,196.19 2640.2,252.32 2788.9,242.21 2980.2,229.16 2980.4,229 2987.7,223.49 2992,214.74 2994.6,206.09", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "chemical entity assesses named thing association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.08 2636.8,252.08 2664.1,250.28 2692,248.53 2718.4,247 2760.4,244.57 3059.6,249.3 3096.4,229 3106.1,223.63 3113.8,214.25 \ +3119.4,205.06", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "chemical entity assesses named thing association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.09 2634.1,251.88 2662.2,250.07 2691.1,248.35 2718.4,247 2750.3,245.42 3264.8,244.95 3292.4,229 3301.6,223.69 3308.4,\ +214.46 3313.3,205.36", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "chemical entity assesses named thing association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.18 2632.7,251.79 2661.3,249.96 2690.7,248.27 2718.4,247 2760.6,245.07 3441.2,248.95 3478.4,229 3488.2,223.75 3495.9,\ +214.39 3501.5,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "chemical entity assesses named thing association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.73 2631.7,251.75 2660.6,249.92 2690.4,248.23 2718.4,247 2769.3,244.77 3590.1,252.38 3635.4,229 3645.7,223.67 3653.9,213.98 \ +3659.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "chemical entity assesses named thing association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.76 2631.4,251.71 2660.4,249.87 2690.3,248.19 2718.4,247 2748,245.74 3757.9,242.22 3784.4,229 3795.1,223.66 3803.8,213.84 \ +3810.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "chemical entity assesses named thing association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2631,251.68 2660.1,249.84 2690.1,248.17 2718.4,247 2752.7,245.58 3923.6,244.1 3954.4,229 3965.2,223.69 3974.1,213.87 \ +3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "chemical entity assesses named thing association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2630.7,251.66 2659.9,249.81 2690,248.15 2718.4,247 2757.2,245.43 4081.5,247.85 4115.4,229 4124.9,223.74 4131.9,214.39 \ +4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "chemical entity assesses named thing association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.2,195.51 1715.7,251.79 1744.3,249.96 1773.7,248.27 1801.4,247 1822.4,246.04 2544.7,244.07 2559.4,229 2565.6,222.65 2565.4,\ -213.6 2562.9,204.95", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2630.4,251.65 2659.7,249.8 2689.9,248.13 2718.4,247 2740,246.14 4258.2,243.28 4274.4,229 4280.9,223.32 4283.4,214.65 \ +4284.1,206.11", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "chemical entity assesses named thing association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.83 1715.4,251.78 1744,249.95 1773.6,248.26 1801.4,247 1845.8,244.99 2560.6,246.68 2601.4,229 2613.8,223.64 2624.6,213.53 \ -2632.9,203.8", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2630.4,251.64 2659.7,249.79 2689.9,248.13 2718.4,247 2762.8,245.24 4277.5,243.88 4319.4,229 4334.6,223.59 4349,212.83 \ +4360.1,202.68", style=solid]; subject [height=0.5, - pos="2764.4,178", + pos="4496.4,178", width=1.2277]; "chemical entity assesses named thing association" -> subject [color=blue, label=subject, - lp="2747.4,221.5", - pos="e,2747.4,194.73 1715.1,251.75 1743.8,249.92 1773.5,248.23 1801.4,247 1850.7,244.82 2643.3,243.94 2690.4,229 2708.4,223.29 2726,211.71 \ -2739.5,201.12", + lp="4473.4,221.5", + pos="e,4477.7,194.32 2630.4,251.63 2659.7,249.78 2689.9,248.12 2718.4,247 2812.5,243.3 4322.8,254.7 4413.4,229 4433.6,223.28 4453.7,211.29 \ +4469.2,200.49", style=solid]; object [height=0.5, - pos="2807.4,91", + pos="4539.4,91", width=1.0832]; "chemical entity assesses named thing association" -> object [color=blue, label=object, - lp="2850.4,178", - pos="e,2820.8,108.09 1714.7,251.73 1743.6,249.89 1773.4,248.21 1801.4,247 1855.6,244.66 2726.5,247.81 2777.4,229 2819.9,213.3 2825.1,\ -186.96 2830.4,142 2831.2,135.38 2832.3,133.39 2830.4,127 2829.4,123.55 2827.9,120.13 2826.1,116.85", + lp="4583.4,178", + pos="e,4552.8,108.09 2630,251.64 2659.4,249.78 2689.8,248.11 2718.4,247 2767.9,245.07 4456.3,244.42 4503.4,229 4527.3,221.18 4535.3,216.87 \ +4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,116.85", style=solid]; predicate [height=0.5, - pos="2961.4,178", + pos="4693.4,178", width=1.5165]; "chemical entity assesses named thing association" -> predicate [color=blue, label=predicate, - lp="2934.4,221.5", - pos="e,2937.6,194.3 1714.4,251.71 1743.4,249.87 1773.3,248.2 1801.4,247 1918.8,242.01 2744.1,256.29 2858.4,229 2883.3,223.06 2909.1,210.47 \ -2928.7,199.4", + lp="4666.4,221.5", + pos="e,4669.6,194.35 2630,251.62 2659.4,249.77 2689.8,248.11 2718.4,247 2822.3,242.97 4489.1,252.79 4590.4,229 4615.3,223.15 4641.2,210.56 \ +4660.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1848.4,265", + pos="2765.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1979.4,265", + pos="2896.4,265", width=2.0762]; subject -> object [label=relation, - lp="2802.4,134.5", - pos="e,2789.5,107.23 2765.5,159.55 2766.7,149.57 2769.2,137.07 2774.4,127 2776.6,122.68 2779.5,118.52 2782.7,114.66"]; + lp="4534.4,134.5", + pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; relation [height=0.5, - pos="2752.4,18", + pos="4484.4,18", width=1.2999]; - subject -> relation [pos="e,2753.7,36.188 2763.1,159.79 2761,132.48 2757,78.994 2754.5,46.38", + subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", style=dotted]; "chemical entity assesses named thing association_subject" [color=blue, height=0.5, label="chemical entity", - pos="2154.4,265", + pos="3071.4,265", width=2.2748]; - object -> relation [pos="e,2765.2,35.54 2794.9,73.889 2788,64.939 2779.2,53.617 2771.4,43.584", + object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", style=dotted]; "chemical entity assesses named thing association_object" [color=blue, height=0.5, label="named thing", - pos="2323.4,265", + pos="3240.4,265", width=1.9318]; "chemical entity assesses named thing association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2489.4,265", + pos="3406.4,265", width=2.1665]; } diff --git a/graphviz/chemical_entity_assesses_named_thing_association.svg b/graphviz/chemical_entity_assesses_named_thing_association.svg index 133072bd4a..dafec5d9bd 100644 --- a/graphviz/chemical_entity_assesses_named_thing_association.svg +++ b/graphviz/chemical_entity_assesses_named_thing_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical entity assesses named thing association - -chemical entity assesses named thing association + +chemical entity assesses named thing association @@ -24,9 +24,9 @@ chemical entity assesses named thing association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ chemical entity assesses named thing association->id - - -id + + +id @@ -50,9 +50,9 @@ chemical entity assesses named thing association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical entity assesses named thing association->name - - -name + + +name @@ -76,9 +76,9 @@ chemical entity assesses named thing association->description - - -description + + +description @@ -89,9 +89,9 @@ chemical entity assesses named thing association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ chemical entity assesses named thing association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical entity assesses named thing association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical entity assesses named thing association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ chemical entity assesses named thing association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ chemical entity assesses named thing association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ chemical entity assesses named thing association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ chemical entity assesses named thing association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ chemical entity assesses named thing association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ chemical entity assesses named thing association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ chemical entity assesses named thing association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ chemical entity assesses named thing association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical entity assesses named thing association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical entity assesses named thing association->object category + + +object category + + + +subject closure + +string + + + +chemical entity assesses named thing association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical entity assesses named thing association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical entity assesses named thing association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical entity assesses named thing association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical entity assesses named thing association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical entity assesses named thing association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical entity assesses named thing association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical entity assesses named thing association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical entity assesses named thing association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical entity assesses named thing association->type - - -type + + +type - + category - -category + +category - + chemical entity assesses named thing association->category - - -category + + +category - + subject - -subject + +subject - + chemical entity assesses named thing association->subject - - -subject + + +subject - + object - -object + +object - + chemical entity assesses named thing association->object - - -object + + +object - + predicate - -predicate + +predicate - + chemical entity assesses named thing association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + chemical entity assesses named thing association_subject - -chemical entity + +chemical entity - + object->relation - - + + - + chemical entity assesses named thing association_object - -named thing + +named thing - + chemical entity assesses named thing association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv index 37f59ba911..f757588143 100644 --- a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv +++ b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3308.9,283"]; + graph [bb="0,0,4996.4,283"]; node [label="\N"]; "chemical entity or gene or gene product regulates gene association" [height=0.5, label="chemical entity or gene or gene product regulates gene association", - pos="1638.4,265", + pos="2531.4,265", width=8.9909]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical entity or gene or gene product regulates gene association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.67 1315.5,263.66 975.47,261.88 462.91,254.79 268.39,229 214.64,221.87 154.52,206.38 113.17,194.52"]; + lp="280.39,221.5", + pos="e,102.91,191.8 2209.5,263.03 1629.8,260.7 453.29,253.04 266.39,229 213.1,222.15 153.57,206.62 112.64,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1321.7,261.24 1013.1,257.43 566.14,248.66 393.39,229 319.52,220.59 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="395.39,221.5", + pos="e,210.38,189.98 2211.7,262.1 1658.3,258.32 563.98,248.48 388.39,229 316.66,221.04 298.9,215.43 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical entity or gene or gene product regulates gene association" -> iri [color=blue, label=iri, - lp="518.39,221.5", - pos="e,315.01,190.16 1328.4,259.78 1050.1,255 662.74,245.63 510.39,229 431.71,220.41 412.11,215.46 335.39,196 331.97,195.13 328.43,194.16 \ -324.9,193.14", + lp="508.39,221.5", + pos="e,315.3,190.19 2213.3,261.67 1684.3,257.32 665.27,246.76 500.39,229 426.04,220.99 407.78,214.78 335.39,196 332.02,195.12 328.54,\ +194.16 325.06,193.14", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "chemical entity or gene or gene product regulates gene association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.02,191.18 1325.2,260.42 1072.4,256.23 737.61,247.36 603.39,229 549.99,221.7 490.22,205.92 449.65,194.03", + lp="615.39,221.5", + pos="e,439.15,191.54 2211.3,262.31 1702.4,259 750.31,250.07 595.39,229 544.62,222.09 488.03,206.58 449.14,194.65", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "chemical entity or gene or gene product regulates gene association" -> description [color=blue, label=description, - lp="742.89,221.5", - pos="e,586.96,193.95 1320.3,261.65 1096.4,258.18 817.01,249.69 702.39,229 665.89,222.41 626.13,208.97 596.57,197.69", + lp="735.89,221.5", + pos="e,585.2,194.15 2208.7,263.36 1721.5,261.55 839.47,254.72 695.39,229 660.55,222.78 622.82,209.42 594.72,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "chemical entity or gene or gene product regulates gene association" -> "has attribute" [color=blue, label="has attribute", - lp="885.39,221.5", - pos="e,726.96,192.73 1328.5,259.78 1144.5,255.45 929.8,246.69 838.39,229 802.93,222.14 764.37,208.11 736.4,196.66", + lp="881.39,221.5", + pos="e,726.02,192.95 2209.3,263.01 1754.6,260.75 965.08,253.34 834.39,229 799.92,222.58 762.64,208.62 735.52,197.07", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical entity or gene or gene product regulates gene association" -> negated [color=blue, label=negated, - lp="1034.4,221.5", - pos="e,847.61,190.33 1336.6,258.46 1231.4,253.59 1112.8,244.77 1005.4,229 953.78,221.42 896.03,205.31 857.47,193.41", + lp="1036.4,221.5", + pos="e,847.24,190.46 2207.8,264.53 1830.7,263.75 1230.8,257.75 1007.4,229 954.83,222.23 896.1,205.81 857.18,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical entity or gene or gene product regulates gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1164.9,221.5", - pos="e,995.68,193.28 1364.2,255.43 1288.4,250.26 1206.4,242.03 1131.4,229 1088.1,221.48 1040.2,207.6 1005.2,196.37", + lp="1174.9,221.5", + pos="e,996.14,193.2 2207.6,264.66 1862.5,263.79 1339.2,257.52 1141.4,229 1094.7,222.26 1042.9,207.87 1005.7,196.25", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical entity or gene or gene product regulates gene association" -> publications [color=blue, label=publications, - lp="1298.4,221.5", - pos="e,1144.8,193.32 1408.6,252.32 1357.4,247.15 1303.8,239.72 1254.4,229 1219.9,221.52 1182.3,208.14 1154.3,197.11", + lp="1320.4,221.5", + pos="e,1147.1,192.85 2207.6,264.73 1896.4,263.65 1448.6,256.98 1276.4,229 1235,222.28 1189.6,207.95 1156.8,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "chemical entity or gene or gene product regulates gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1437.9,221.5", - pos="e,1299.3,194.37 1490.3,248.97 1457.4,243.99 1423,237.47 1391.4,229 1363,221.39 1332.4,209.08 1308.7,198.58", + lp="1478.9,221.5", + pos="e,1305.4,193.63 2209.5,263.06 1939.7,260.55 1576.3,252.66 1432.4,229 1392,222.35 1347.6,208.52 1315.1,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "chemical entity or gene or gene product regulates gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1566.9,221.5", - pos="e,1476.8,196.24 1539.4,247.81 1526.3,243.06 1513.5,236.93 1502.4,229 1493.8,222.9 1486.9,213.84 1481.6,205.1", + lp="1633.9,221.5", + pos="e,1494.9,195.61 2224,259.33 1966.7,254.34 1631.7,244.91 1569.4,229 1546.3,223.1 1522.3,211.34 1503.6,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "chemical entity or gene or gene product regulates gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1734.4,221.5", - pos="e,1660,194.65 1634.6,246.59 1633.3,236.37 1633.5,223.63 1639.4,214 1642.6,208.82 1646.8,204.35 1651.6,200.52", + lp="1805.4,221.5", + pos="e,1701.4,196.33 2220.1,260.02 1995.9,255.65 1729.6,246.76 1710.4,229 1704.3,223.32 1701.9,214.91 1701.3,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -130,9 +130,8 @@ digraph { width=3.015]; "chemical entity or gene or gene product regulates gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1958.9,221.5", - pos="e,1895.7,194.64 1763.7,248.4 1786,243.56 1808.7,237.24 1829.4,229 1840.7,224.48 1841.6,219.64 1852.4,214 1863.1,208.42 1874.9,203.13 \ -1886.3,198.44", + lp="2013.9,221.5", + pos="e,1917.6,195.87 2245.4,256.57 2087.1,251.01 1919.8,242.08 1907.4,229 1900.2,221.43 1903.7,212.05 1910.6,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -141,8 +140,8 @@ digraph { width=1.5346]; "chemical entity or gene or gene product regulates gene association" -> timepoint [color=blue, label=timepoint, - lp="2119.4,221.5", - pos="e,2105.4,195.38 1860.8,251.9 1953.9,245.68 2045.3,237.61 2065.4,229 2072.8,225.82 2086.2,214.01 2098,202.67", + lp="2168.4,221.5", + pos="e,2120.8,196.43 2282.8,253.46 2210.1,248.14 2146.5,240.32 2133.4,229 2126.9,223.36 2123.5,214.85 2122,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -151,8 +150,8 @@ digraph { width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "original subject" [color=blue, label="original subject", - lp="2236.4,221.5", - pos="e,2212.3,193.27 1858.2,251.77 1993.4,243.82 2143.6,234.03 2158.4,229 2159.7,228.55 2183.4,212.7 2203.8,198.97", + lp="2266.4,221.5", + pos="e,2217.6,194.82 2318.6,251.43 2264.6,246.09 2219.2,238.78 2210.4,229 2203.7,221.56 2206.3,211.86 2211.8,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -161,8 +160,8 @@ digraph { width=1.5887]; "chemical entity or gene or gene product regulates gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2376.9,221.5", - pos="e,2332.1,195.44 1867.2,252.22 2055.1,242.48 2290.9,230.07 2293.4,229 2300.7,225.92 2313.6,214.11 2324.9,202.75", + lp="2392.9,221.5", + pos="e,2333.6,195.8 2373.3,249.17 2353,244.26 2336.7,237.71 2329.4,229 2323.5,222.05 2324.9,213.06 2328.7,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -171,102 +170,217 @@ digraph { width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "original object" [color=blue, label="original object", - lp="2506.9,221.5", - pos="e,2460,196.28 1864.1,252.08 1900,250.3 1936.7,248.55 1971.4,247 1997.6,245.83 2422.2,244.5 2443.4,229 2450.8,223.6 2455.1,214.87 \ -2457.7,206.22", + lp="2516.9,221.5", + pos="e,2458.9,196.07 2484.7,247.02 2477.2,242.29 2470.2,236.37 2465.4,229 2461,222.32 2459.2,214 2458.8,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "chemical entity or gene or gene product regulates gene association" -> "subject category" [color=blue, + label="subject category", + lp="2640.9,221.5", + pos="e,2589,196.22 2555.3,246.74 2561.4,241.53 2567.6,235.46 2572.4,229 2577.6,221.97 2581.9,213.49 2585.3,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "chemical entity or gene or gene product regulates gene association" -> "object category" [color=blue, + label="object category", + lp="2783.9,221.5", + pos="e,2749.3,195.91 2649.3,248.2 2668.2,243.4 2687.2,237.15 2704.4,229 2718,222.54 2731.2,212.41 2741.8,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "chemical entity or gene or gene product regulates gene association" -> "subject closure" [color=blue, + label="subject closure", + lp="2920.9,221.5", + pos="e,2885.3,195.42 2733.6,250.93 2780.1,245.74 2822.1,238.63 2843.4,229 2856.6,223.04 2868.7,212.72 2878.3,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "chemical entity or gene or gene product regulates gene association" -> "object closure" [color=blue, + label="object closure", + lp="3041.4,221.5", + pos="e,2996.5,196.18 2752.4,251.83 2860.4,244.99 2969.5,236.38 2979.4,229 2986.8,223.48 2991.3,214.73 2994,206.08", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "chemical entity or gene or gene product regulates gene association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3199.9,221.5", + pos="e,3124,196.04 2758,252.13 2911.4,243.73 3087.7,233.25 3095.4,229 3105.2,223.57 3113.1,214.19 3118.9,205", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "chemical entity or gene or gene product regulates gene association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.3,196.06 2758.4,252.14 2793.9,250.36 2830.1,248.6 2864.4,247 2911.8,244.79 3250.2,252.67 3291.4,229 3300.8,223.61 3307.8,\ +214.23 3312.9,205.04", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "chemical entity or gene or gene product regulates gene association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.16 2754.4,251.95 2791.1,250.15 2828.8,248.43 2864.4,247 2898.5,245.63 3448.4,245.2 3478.4,229 3488.2,223.72 3495.8,\ +214.36 3501.4,205.15", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "chemical entity or gene or gene product regulates gene association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.71 2752.6,251.85 2789.9,250.05 2828.2,248.34 2864.4,247 2907.2,245.41 3597.4,248.73 3635.4,229 3645.7,223.65 3653.9,213.96 \ +3659.9,204.53", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "chemical entity or gene or gene product regulates gene association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.75 2751.7,251.78 2789.3,249.97 2827.9,248.29 2864.4,247 2915.5,245.2 3738.7,251.88 3784.4,229 3795.1,223.64 3803.7,\ +213.82 3810.1,204.29", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "chemical entity or gene or gene product regulates gene association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.78 2750.8,251.72 2788.7,249.91 2827.7,248.24 2864.4,247 2894.7,245.98 3927.2,242.34 3954.4,229 3965.2,223.67 3974.1,\ +213.85 3980.7,204.32", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4138.4,178", + width=2.347]; + "chemical entity or gene or gene product regulates gene association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4197.9,221.5", + pos="e,4135.4,196 2749.9,251.7 2788,249.88 2827.4,248.21 2864.4,247 2899.1,245.86 4086.3,247.96 4115.4,229 4123.5,223.7 4128.8,214.72 \ +4132.3,205.81", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4272.4,178", width=0.86659]; "chemical entity or gene or gene product regulates gene association" -> type [color=blue, label=type, - lp="2583.4,221.5", - pos="e,2560.4,194.94 1861.8,251.96 1898.4,250.17 1936,248.44 1971.4,247 2004.2,245.66 2539.5,252.58 2562.4,229 2568.8,222.38 2568,213.01 \ -2564.7,204.17", + lp="4294.4,221.5", + pos="e,4277.5,196.18 2749.4,251.67 2787.7,249.85 2827.2,248.19 2864.4,247 2883.9,246.38 4257.5,242.77 4271.4,229 4277.4,223.09 4279,214.51 \ +4278.6,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4373.4,178", width=1.4263]; "chemical entity or gene or gene product regulates gene association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.9,195.79 1861.4,251.92 1898.1,250.13 1935.8,248.41 1971.4,247 2006.5,245.6 2571.4,243.4 2603.4,229 2615.4,223.58 2625.9,213.47 \ -2633.8,203.75", + lp="4371.9,221.5", + pos="e,4359.8,195.45 2749.4,251.66 2787.7,249.84 2827.2,248.18 2864.4,247 2904.7,245.72 4276.7,243.1 4314.4,229 4329,223.55 4342.4,212.79 \ +4352.8,202.65", style=solid]; "object direction qualifier" [height=0.5, - pos="2844.4,178", + pos="4567.4,178", width=3.4664]; "chemical entity or gene or gene product regulates gene association" -> "object direction qualifier" [color=blue, label="object direction qualifier", - lp="2839.4,221.5", - pos="e,2805.3,195.17 1860,251.88 1897.2,250.08 1935.4,248.37 1971.4,247 2131.1,240.93 2532.9,255.96 2690.4,229 2726.6,222.8 2766.1,209.87 \ -2796,198.72", + lp="4558.4,221.5", + pos="e,4527.4,195.08 2749,251.66 2787.4,249.83 2827.1,248.17 2864.4,247 3035.8,241.63 4238.1,255.85 4407.4,229 4445.3,222.99 4486.5,209.93 \ +4517.7,198.66", style=solid]; predicate [height=0.5, - pos="3041.4,178", + pos="4764.4,178", width=1.5165]; "chemical entity or gene or gene product regulates gene association" -> predicate [color=blue, label=predicate, - lp="3009.4,221.5", - pos="e,3016.2,194.04 1858.2,251.77 1896,249.96 1934.8,248.28 1971.4,247 2078,243.28 2827.3,252.56 2931.4,229 2958.1,222.95 2986.2,210.05 \ -3007.3,198.87", + lp="4730.4,221.5", + pos="e,4738.2,194.11 2748.5,251.63 2787.1,249.8 2826.9,248.14 2864.4,247 2963.6,243.97 4553.4,249.85 4650.4,229 4678.1,223.04 4707.4,\ +210.05 4729.3,198.8", style=solid]; subject [height=0.5, - pos="3158.4,178", + pos="4881.4,178", width=1.2277]; "chemical entity or gene or gene product regulates gene association" -> subject [color=blue, label=subject, - lp="3118.4,221.5", - pos="e,3134.3,193.34 1857.8,251.73 1895.7,249.92 1934.7,248.24 1971.4,247 2090.9,242.95 2930.7,255.09 3047.4,229 3074.9,222.85 3103.8,\ -209.55 3125.3,198.22", + lp="4839.4,221.5", + pos="e,4857.3,193.16 2748.5,251.61 2787.1,249.78 2826.9,248.13 2864.4,247 2970.1,243.8 4665,251.36 4768.4,229 4796.6,222.89 4826.5,209.36 \ +4848.4,197.91", style=solid]; object [height=0.5, - pos="3201.4,91", + pos="4924.4,91", width=1.0832]; "chemical entity or gene or gene product regulates gene association" -> object [color=blue, label=object, - lp="3251.4,178", - pos="e,3214.8,108.09 1857.3,251.71 1895.3,249.89 1934.5,248.22 1971.4,247 2036.8,244.83 3085,245.11 3148.4,229 3179,221.21 3192,220.93 \ -3211.4,196 3230.6,171.39 3233.3,156.9 3224.4,127 3223.4,123.55 3221.9,120.13 3220.1,116.85", + lp="4974.4,178", + pos="e,4937.8,108.09 2748.1,251.62 2786.8,249.78 2826.8,248.13 2864.4,247 2975.7,243.66 4761.2,255.41 4869.4,229 4900.9,221.32 4914.3,\ +221.42 4934.4,196 4953.7,171.51 4956.3,156.9 4947.4,127 4946.4,123.55 4944.9,120.13 4943.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2018.4,265", + pos="2911.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2149.4,265", + pos="3042.4,265", width=2.0762]; "chemical entity or gene or gene product regulates gene association_object direction qualifier" [color=blue, height=0.5, label=DirectionQualifierEnum, - pos="2363.4,265", + pos="3256.4,265", width=3.358]; "chemical entity or gene or gene product regulates gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2580.4,265", + pos="3473.4,265", width=2.1665]; subject -> object [label=relation, - lp="3196.4,134.5", - pos="e,3183.5,107.23 3159.5,159.55 3160.7,149.57 3163.2,137.07 3168.4,127 3170.6,122.68 3173.5,118.52 3176.7,114.66"]; + lp="4919.4,134.5", + pos="e,4906.5,107.23 4882.5,159.55 4883.7,149.57 4886.2,137.07 4891.4,127 4893.6,122.68 4896.5,118.52 4899.7,114.66"]; relation [height=0.5, - pos="3146.4,18", + pos="4869.4,18", width=1.2999]; - subject -> relation [pos="e,3147.7,36.188 3157.1,159.79 3155,132.48 3151,78.994 3148.5,46.38", + subject -> relation [pos="e,4870.7,36.188 4880.1,159.79 4878,132.48 4874,78.994 4871.5,46.38", style=dotted]; "chemical entity or gene or gene product regulates gene association_subject" [color=blue, height=0.5, label="chemical entity or gene or gene product", - pos="2873.4,265", + pos="3766.4,265", width=5.4703]; - object -> relation [pos="e,3159.2,35.54 3188.9,73.889 3182,64.939 3173.2,53.617 3165.4,43.584", + object -> relation [pos="e,4882.2,35.54 4911.9,73.889 4905,64.939 4896.2,53.617 4888.4,43.584", style=dotted]; "chemical entity or gene or gene product regulates gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3198.4,265", + pos="4091.4,265", width=3.0692]; } diff --git a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg index 5e55232b14..03f7ad1888 100644 --- a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg +++ b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical entity or gene or gene product regulates gene association - -chemical entity or gene or gene product regulates gene association + +chemical entity or gene or gene product regulates gene association @@ -24,9 +24,9 @@ chemical entity or gene or gene product regulates gene association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ chemical entity or gene or gene product regulates gene association->id - - -id + + +id @@ -50,9 +50,9 @@ chemical entity or gene or gene product regulates gene association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical entity or gene or gene product regulates gene association->name - - -name + + +name @@ -76,9 +76,9 @@ chemical entity or gene or gene product regulates gene association->description - - -description + + +description @@ -89,9 +89,9 @@ chemical entity or gene or gene product regulates gene association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ chemical entity or gene or gene product regulates gene association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical entity or gene or gene product regulates gene association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical entity or gene or gene product regulates gene association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ chemical entity or gene or gene product regulates gene association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ chemical entity or gene or gene product regulates gene association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ chemical entity or gene or gene product regulates gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ chemical entity or gene or gene product regulates gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ chemical entity or gene or gene product regulates gene association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ chemical entity or gene or gene product regulates gene association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ chemical entity or gene or gene product regulates gene association->original predicate - - -original predicate + + +original predicate @@ -232,148 +232,291 @@ chemical entity or gene or gene product regulates gene association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical entity or gene or gene product regulates gene association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical entity or gene or gene product regulates gene association->object category + + +object category + + + +subject closure + +string + + + +chemical entity or gene or gene product regulates gene association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical entity or gene or gene product regulates gene association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical entity or gene or gene product regulates gene association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical entity or gene or gene product regulates gene association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical entity or gene or gene product regulates gene association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical entity or gene or gene product regulates gene association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical entity or gene or gene product regulates gene association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical entity or gene or gene product regulates gene association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical entity or gene or gene product regulates gene association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical entity or gene or gene product regulates gene association->type - - -type + + +type - + category - -category + +category - + chemical entity or gene or gene product regulates gene association->category - - -category + + +category - + object direction qualifier - -object direction qualifier + +object direction qualifier - + chemical entity or gene or gene product regulates gene association->object direction qualifier - - -object direction qualifier + + +object direction qualifier - + predicate - -predicate + +predicate - + chemical entity or gene or gene product regulates gene association->predicate - - -predicate + + +predicate - + subject - -subject + +subject - + chemical entity or gene or gene product regulates gene association->subject - - -subject + + +subject - + object - -object + +object - + chemical entity or gene or gene product regulates gene association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + chemical entity or gene or gene product regulates gene association_object direction qualifier - -DirectionQualifierEnum + +DirectionQualifierEnum - + chemical entity or gene or gene product regulates gene association_predicate - -predicate type + +predicate type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + chemical entity or gene or gene product regulates gene association_subject - -chemical entity or gene or gene product + +chemical entity or gene or gene product - + object->relation - - + + - + chemical entity or gene or gene product regulates gene association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/chemical_gene_interaction_association.gv b/graphviz/chemical_gene_interaction_association.gv index 64eb006d53..cc8e289b36 100644 --- a/graphviz/chemical_gene_interaction_association.gv +++ b/graphviz/chemical_gene_interaction_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,6664.4,283"]; + graph [bb="0,0,7388.4,283"]; node [label="\N"]; "chemical gene interaction association" [height=0.5, label="chemical gene interaction association", - pos="2585.4,265", + pos="3309.4,265", width=5.1454]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical gene interaction association" -> association [label=is_a, lp="495.39,221.5", - pos="e,107.14,190.57 2401.4,262.79 1960.4,259.58 852.08,249.68 481.39,229 326.72,220.37 287.25,221.19 134.39,196 128.71,195.06 122.81,\ -193.93 116.94,192.71"]; + pos="e,107.14,190.57 3124.5,263.71 2581.6,262.52 998.21,256.73 481.39,229 326.7,220.7 287.25,221.19 134.39,196 128.71,195.06 122.81,193.93 \ +116.94,192.71"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical gene interaction association" -> "chemical to entity association mixin" [label=uses, lp="650.89,221.5", - pos="e,397.12,194.3 2400.1,263.99 1981.6,263.42 973.33,258.88 634.39,229 557.02,222.18 469.83,207.75 406.99,196.14"]; + pos="e,396.47,194.28 3124.7,263.13 2560.1,260.27 880.16,250.06 634.39,229 556.74,222.34 469.22,207.82 406.35,196.13"]; id [color=blue, height=0.5, label=string, @@ -26,7 +26,7 @@ digraph { "chemical gene interaction association" -> id [color=blue, label=id, lp="769.39,221.5", - pos="e,583.38,189.98 2399.9,264.77 2001.6,265.72 1075.1,263.95 762.39,229 690.24,220.94 672.34,215.5 602.39,196 599.29,195.13 596.09,\ + pos="e,583.38,189.98 3124.4,263.49 2577.9,261.68 994.57,254.31 762.39,229 690.21,221.13 672.34,215.5 602.39,196 599.29,195.13 596.09,\ 194.17 592.89,193.15", style=solid]; iri [color=blue, @@ -36,8 +36,8 @@ digraph { width=1.2277]; "chemical gene interaction association" -> iri [color=blue, label=iri, - lp="883.39,221.5", - pos="e,688.3,190.2 2400,264.29 2020.4,264.22 1165.9,260.43 875.39,229 800.18,220.86 781.65,214.92 708.39,196 705.02,195.13 701.54,194.16 \ + lp="882.39,221.5", + pos="e,688.3,190.2 3124.6,263.28 2594.9,260.95 1095.3,252.35 874.39,229 799.59,221.09 781.22,214.85 708.39,196 705.02,195.13 701.54,194.16 \ 698.06,193.15", style=solid]; name [color=blue, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "chemical gene interaction association" -> name [color=blue, label=name, - lp="991.39,221.5", - pos="e,812.39,191.41 2401.9,262.35 2008.8,258.47 1109.6,247.67 971.39,229 919.49,221.99 861.56,206.3 822.03,194.35", + lp="989.39,221.5", + pos="e,811.98,191.47 3124.4,263.74 2608.9,262.65 1180,257.11 969.39,229 918.09,222.15 860.88,206.49 821.77,194.51", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "chemical gene interaction association" -> description [color=blue, label=description, - lp="1113.9,221.5", - pos="e,959.14,193.99 2401.4,262.83 2027,260.01 1200.7,251.31 1073.4,229 1037.2,222.65 997.8,209.13 968.62,197.75", + lp="1109.9,221.5", + pos="e,958.44,194.19 3124.1,264.46 2623.7,265.22 1268.7,263.99 1069.4,229 1034.3,222.84 996.32,209.47 968.03,198.11", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "chemical gene interaction association" -> "has attribute" [color=blue, label="has attribute", - lp="1261.4,221.5", - pos="e,1100.1,192.66 2401.8,262.44 2054.9,259.02 1327.9,249.51 1214.4,229 1177.8,222.38 1138,208.1 1109.3,196.48", + lp="1255.4,221.5", + pos="e,1099,192.87 3124,264.38 2645.6,264.88 1393.5,262.88 1208.4,229 1173.4,222.6 1135.6,208.47 1108.2,196.85", style=solid]; negated [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.2999]; "chemical gene interaction association" -> negated [color=blue, label=negated, - lp="1420.4,221.5", - pos="e,1221.1,190.1 2401.3,262.81 2116.2,260.26 1581,252.43 1391.4,229 1335.1,222.05 1272,205.23 1230.8,193.02", + lp="1410.4,221.5", + pos="e,1220.4,190.52 3125.3,262.89 2676.6,259.88 1551,250.28 1381.4,229 1328.4,222.36 1269.3,205.85 1230.2,193.61", style=solid]; qualifiers [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1304]; "chemical gene interaction association" -> qualifiers [color=blue, label=qualifiers, - lp="1557.9,221.5", - pos="e,1371.1,192.97 2401.7,262.71 2143.9,260.08 1688.2,252.21 1524.4,229 1475,221.99 1420,207.46 1380.7,195.85", + lp="1549.9,221.5", + pos="e,1369.2,193.15 3125.3,262.9 2699.7,260 1672.2,250.81 1516.4,229 1469,222.37 1416.5,207.89 1378.9,196.21", style=solid]; publications [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.7332]; "chemical gene interaction association" -> publications [color=blue, label=publications, - lp="1701.4,221.5", - pos="e,1521.6,192.61 2401.9,262.37 2173.2,259.41 1795.6,251.23 1657.4,229 1613.8,221.99 1565.8,207.53 1531.4,195.95", + lp="1697.4,221.5", + pos="e,1520.7,192.8 3125.2,262.87 2724,260.01 1795.3,251.08 1653.4,229 1610.7,222.36 1563.8,207.86 1530.2,196.17", style=solid]; "has evidence" [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.0943]; "chemical gene interaction association" -> "has evidence" [color=blue, label="has evidence", - lp="1857.9,221.5", - pos="e,1679.8,193.47 2405.2,260.83 2213,256.56 1921.3,247.28 1811.4,229 1769.5,222.03 1723.3,208.13 1689.5,196.75", + lp="1858.9,221.5", + pos="e,1679.4,193.48 3125.9,262.37 2754.6,258.7 1938.7,248.5 1812.4,229 1769.9,222.44 1723.1,208.37 1689,196.82", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=3.015]; "chemical gene interaction association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2010.9,221.5", - pos="e,1869.1,195.46 2402.5,261.92 2244.7,258.67 2029.5,250.34 1946.4,229 1922.4,222.85 1897.4,211 1877.9,200.38", + lp="2016.9,221.5", + pos="e,1870.2,195.45 3124.8,263.33 2780.1,261.46 2063.4,254.54 1952.4,229 1926.9,223.12 1900.1,211.08 1879.3,200.29", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -127,8 +127,8 @@ digraph { width=3.015]; "chemical gene interaction association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2183.4,221.5", - pos="e,2076.3,196.45 2403.2,261.62 2271.4,258.16 2112.4,249.69 2088.4,229 2081.9,223.38 2078.7,214.88 2077.3,206.47", + lp="2191.4,221.5", + pos="e,2079.1,196.34 3124.4,264.02 2795,263.31 2137.5,258.21 2096.4,229 2088.9,223.66 2084.3,214.95 2081.6,206.29", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -137,8 +137,8 @@ digraph { width=3.015]; "chemical gene interaction association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2391.9,221.5", - pos="e,2293.4,195.98 2431.5,254.92 2363.3,249.28 2295.9,240.82 2285.4,229 2278.8,221.63 2281.5,212.38 2287.2,203.86", + lp="2400.9,221.5", + pos="e,2298.2,196.19 3124.2,264.18 2839.1,263.53 2322.7,258.29 2294.4,229 2288.1,222.47 2289.3,213.57 2293.2,205.09", style=solid]; timepoint [color=blue, height=0.5, @@ -147,8 +147,8 @@ digraph { width=1.5346]; "chemical gene interaction association" -> timepoint [color=blue, label=timepoint, - lp="2545.4,221.5", - pos="e,2496.3,196 2535.1,247.58 2525.9,242.76 2517.1,236.66 2510.4,229 2504.7,222.56 2501.1,214.08 2498.7,205.95", + lp="2560.4,221.5", + pos="e,2500.1,196.04 3124.1,264.73 2908.6,264.18 2575.6,258.46 2525.4,229 2516.2,223.63 2509.4,214.39 2504.5,205.29", style=solid]; "original subject" [color=blue, height=0.5, @@ -157,8 +157,8 @@ digraph { width=1.0652]; "chemical gene interaction association" -> "original subject" [color=blue, label="original subject", - lp="2642.4,221.5", - pos="e,2594.8,195.34 2583.7,246.57 2583.2,236.82 2583.5,224.54 2586.4,214 2587.3,210.76 2588.6,207.51 2590,204.36", + lp="2661.4,221.5", + pos="e,2600.6,196.02 3128.3,261.14 2925.7,257.02 2623.3,247.77 2605.4,229 2599.6,222.92 2598.3,214.3 2599,205.92", style=solid]; "original predicate" [color=blue, height=0.5, @@ -167,8 +167,8 @@ digraph { width=1.5887]; "chemical gene interaction association" -> "original predicate" [color=blue, label="original predicate", - lp="2772.9,221.5", - pos="e,2716.8,196 2665.6,248.65 2677.5,243.79 2689,237.41 2698.4,229 2705.3,222.83 2710.2,214.08 2713.5,205.62", + lp="2792.9,221.5", + pos="e,2718.6,196.41 3124.2,264.09 2965.7,262.34 2758.7,255.01 2729.4,229 2723,223.34 2720.2,214.82 2719.1,206.41", style=solid]; "original object" [color=blue, height=0.5, @@ -177,198 +177,314 @@ digraph { width=1.0652]; "chemical gene interaction association" -> "original object" [color=blue, label="original object", - lp="2897.9,221.5", - pos="e,2842.3,195.75 2722.4,252.89 2778.3,246.94 2831.8,238.81 2840.4,229 2846,222.63 2846.5,213.94 2844.9,205.59", + lp="2929.9,221.5", + pos="e,2844.1,195.53 3125.5,262.64 3028.7,259.26 2921.3,250.51 2878.4,229 2867,223.3 2857.3,213.29 2849.9,203.72", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2967.4,178", + width=2.1304]; + "chemical gene interaction association" -> "subject category" [color=blue, + label="subject category", + lp="3059.9,221.5", + pos="e,2974.2,196.29 3141,257.47 3082.2,252.57 3024.8,243.99 3000.4,229 2991.3,223.43 2984.2,214.31 2979,205.38", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3138.4,178", + width=2.1304]; + "chemical gene interaction association" -> "object category" [color=blue, + label="object category", + lp="3182.9,221.5", + pos="e,3128.1,195.99 3183.6,251.66 3157.8,246.51 3135.8,239.23 3127.4,229 3121.9,222.4 3122.2,213.69 3124.5,205.39", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3271.4,178", + width=1.0652]; + "chemical gene interaction association" -> "subject closure" [color=blue, + label="subject closure", + lp="3298.9,221.5", + pos="e,3254.2,194.51 3263.3,247.41 3255.7,242.63 3248.9,236.59 3244.4,229 3239.3,220.49 3242.4,210.95 3248,202.51", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3371.4,178", + width=1.0652]; + "chemical gene interaction association" -> "object closure" [color=blue, + label="object closure", + lp="3411.4,221.5", + pos="e,3367.7,196.33 3335.8,246.85 3342.2,241.72 3348.6,235.66 3353.4,229 3358.3,222.15 3362,213.81 3364.7,205.93", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3504.4,178", + width=2.1304]; + "chemical gene interaction association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3569.9,221.5", + pos="e,3495.4,195.9 3416.5,250.27 3433.7,245.23 3450.6,238.36 3465.4,229 3475.1,222.84 3483.4,213.37 3489.8,204.32", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3696.4,178", + width=2.1304]; + "chemical gene interaction association" -> "object category closure" [color=blue, + label="object category closure", + lp="3760.9,221.5", + pos="e,3689,196.37 3440.4,252.24 3538.4,243.23 3656.5,231.88 3661.4,229 3670.9,223.46 3678.4,214.23 3684,205.19", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3886.4,178", + width=1.0652]; + "chemical gene interaction association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3933.4,221.5", + pos="e,3878.4,196.1 3438.6,252.1 3460.6,250.26 3483.1,248.48 3504.4,247 3542.6,244.34 3814.6,246.9 3848.4,229 3858.6,223.59 3866.9,214.08 \ +3873.1,204.79", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4045.4,178", + width=1.0652]; + "chemical gene interaction association" -> "object namespace" [color=blue, + label="object namespace", + lp="4087.4,221.5", + pos="e,4037.1,195.7 3437,251.93 3459.5,250.08 3482.6,248.34 3504.4,247 3560,243.58 3955.6,254.03 4005.4,229 4016.2,223.57 4025,213.73 \ +4031.6,204.21", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4140.4,178", + width=1.0652]; + "chemical gene interaction association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4234.4,221.5", + pos="e,4152.6,195.36 3436.2,251.84 3458.9,249.98 3482.3,248.27 3504.4,247 3522.5,245.96 4142.8,241.97 4155.4,229 4161.8,222.42 4160.8,\ +213.21 4157.2,204.49", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4235.4,178", + width=1.0652]; + "chemical gene interaction association" -> "object label closure" [color=blue, + label="object label closure", + lp="4385.9,221.5", + pos="e,4263.8,190.16 3435.4,251.81 3458.4,249.93 3482.1,248.22 3504.4,247 3526.8,245.77 4296.7,245.05 4312.4,229 4317.1,224.23 4316,219.61 \ +4312.4,214 4309.9,210.14 4291.4,201.68 4273.2,194.05", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4376.4,178", + width=2.347]; + "chemical gene interaction association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4534.9,221.5", + pos="e,4428.6,192.27 3435.2,251.77 3458.2,249.89 3482,248.19 3504.4,247 3530.9,245.6 4440.8,247.94 4459.4,229 4472.6,215.57 4458.4,204.33 \ +4438.2,195.93", style=solid]; type [height=0.5, - pos="2922.4,178", + pos="4510.4,178", width=0.86659]; "chemical gene interaction association" -> type [color=blue, label=type, - lp="2973.4,221.5", - pos="e,2940.7,193.09 2718,252.41 2822.6,243.11 2951.3,231.25 2953.4,229 2961.2,220.41 2956,209.6 2947.7,200.23", + lp="4628.4,221.5", + pos="e,4534.5,189.42 3434.9,251.74 3458,249.86 3481.9,248.16 3504.4,247 3535,245.42 4586.9,250.86 4608.4,229 4613.1,224.25 4612.3,219.38 \ +4608.4,214 4592.7,192.57 4576.4,205.1 4551.4,196 4549,195.12 4546.5,194.19 4544,193.22", style=solid]; category [height=0.5, - pos="3023.4,178", + pos="4611.4,178", width=1.4263]; "chemical gene interaction association" -> category [color=blue, label=category, - lp="3039.9,221.5", - pos="e,3017.7,196.37 2717.8,252.41 2738.8,250.59 2760.2,248.74 2780.4,247 2827.7,242.94 2953.1,254.13 2993.4,229 3002.2,223.52 3008.8,\ -214.42 3013.5,205.47", + lp="4684.9,221.5", + pos="e,4634.4,194.31 3434.9,251.73 3458,249.85 3481.9,248.16 3504.4,247 3536.1,245.37 4626.1,251.65 4648.4,229 4656.7,220.54 4651.1,210.12 \ +4641.9,200.99", style=solid]; "subject form or variant qualifier" [height=0.5, - pos="3252.4,178", + pos="4840.4,178", width=4.4232]; "chemical gene interaction association" -> "subject form or variant qualifier" [color=blue, label="subject form or variant qualifier", - lp="3254.9,221.5", - pos="e,3205.3,195.28 2715.7,252.17 2737.3,250.34 2759.5,248.55 2780.4,247 2911.4,237.3 2945.9,250.98 3075.4,229 3116.2,222.07 3161.1,\ -209.33 3195.5,198.44", + lp="4882.9,221.5", + pos="e,4809.4,195.79 3434.7,251.73 3457.8,249.85 3481.8,248.15 3504.4,247 3639.3,240.13 4588.1,256.48 4720.4,229 4748.2,223.23 4777.6,\ +211.08 4800.4,200.19", style=solid]; "subject part qualifier" [height=0.5, - pos="3538.4,178", + pos="5126.4,178", width=3.015]; "chemical gene interaction association" -> "subject part qualifier" [color=blue, label="subject part qualifier", - lp="3513.9,221.5", - pos="e,3497.4,194.73 2712.5,251.87 2735.1,250.01 2758.4,248.29 2780.4,247 2912,239.27 3243.3,250.3 3373.4,229 3412.6,222.58 3455.5,209.37 \ -3487.8,198.14", + lp="5126.9,221.5", + pos="e,5095,195.32 3434.4,251.7 3457.6,249.81 3481.7,248.12 3504.4,247 3587.5,242.89 4919.8,245.22 5001.4,229 5030.7,223.17 5062,210.66 \ +5085.9,199.62", style=solid]; "subject derivative qualifier" [height=0.5, - pos="3800.4,178", + pos="5388.4,178", width=3.7733]; "chemical gene interaction association" -> "subject derivative qualifier" [color=blue, label="subject derivative qualifier", - lp="3770.9,221.5", - pos="e,3748.7,194.78 2711.4,251.81 2734.4,249.93 2758.1,248.22 2780.4,247 2960.8,237.15 3414.2,252.35 3593.4,229 3643,222.53 3698,208.93 \ -3738.9,197.54", + lp="5373.9,221.5", + pos="e,5342.7,195.08 3434.4,251.68 3457.6,249.79 3481.7,248.11 3504.4,247 3693.3,237.78 5019.1,255.27 5206.4,229 5249.7,222.93 5297.3,\ +209.6 5333,198.23", style=solid]; "subject context qualifier" [height=0.5, - pos="4077.4,178", + pos="5665.4,178", width=3.4303]; "chemical gene interaction association" -> "subject context qualifier" [color=blue, label="subject context qualifier", - lp="4039.4,221.5", - pos="e,4027.2,194.5 2710.9,251.74 2734,249.86 2757.9,248.16 2780.4,247 3022.5,234.46 3630.9,259.79 3871.4,229 3921.3,222.61 3976.7,208.78 \ -4017.4,197.29", + lp="5636.4,221.5", + pos="e,5618.6,194.73 3434.1,251.67 3457.5,249.78 3481.7,248.09 3504.4,247 3723,236.49 5257.4,257.94 5474.4,229 5520.4,222.86 5571.2,209.23 \ +5608.8,197.75", style=solid]; "object form or variant qualifier" [height=0.5, - pos="4373.4,178", + pos="5961.4,178", width=4.2788]; "chemical gene interaction association" -> "object form or variant qualifier" [color=blue, label="object form or variant qualifier", - lp="4335.9,221.5", - pos="e,4313.5,194.64 2710.7,251.71 2733.8,249.82 2757.8,248.13 2780.4,247 3080,231.96 3832.1,261.38 4130.4,229 4189.5,222.59 4255.5,208.56 \ -4303.8,196.99", + lp="5928.9,221.5", + pos="e,5903.7,194.73 3434.1,251.65 3457.5,249.76 3481.7,248.08 3504.4,247 3751.1,235.26 5481.9,255.95 5727.4,229 5784.1,222.77 5847.4,\ +208.82 5893.8,197.24", style=solid]; "object part qualifier" [height=0.5, - pos="4648.4,178", + pos="6236.4,178", width=2.8525]; "chemical gene interaction association" -> "object part qualifier" [color=blue, label="object part qualifier", - lp="4599.4,221.5", - pos="e,4601.8,194.1 2710.4,251.68 2733.6,249.79 2757.7,248.11 2780.4,247 2965.7,237.94 4266.4,252.88 4450.4,229 4499,222.69 4552.9,208.61 \ -4592.1,196.99", + lp="6190.4,221.5", + pos="e,6191,194.15 3433.9,251.66 3457.3,249.76 3481.6,248.07 3504.4,247 3645.3,240.37 5903.5,247.33 6043.4,229 6090.7,222.81 6142.9,208.81 \ +6181.1,197.2", style=solid]; "object context qualifier" [height=0.5, - pos="4887.4,178", + pos="6475.4,178", width=3.2858]; "chemical gene interaction association" -> "object context qualifier" [color=blue, label="object context qualifier", - lp="4840.4,221.5", - pos="e,4836.3,194.35 2710.1,251.68 2733.5,249.79 2757.7,248.1 2780.4,247 2990.6,236.85 4465.5,254.2 4674.4,229 4726.4,222.73 4784.2,208.7 \ -4826.5,197.09", + lp="6430.4,221.5", + pos="e,6425.1,194.4 3433.9,251.64 3457.3,249.75 3481.6,248.07 3504.4,247 3657.6,239.83 6113.1,247.38 6265.4,229 6316.7,222.8 6373.7,208.77 \ +6415.3,197.14", style=solid]; "anatomical context qualifier" [height=0.5, - pos="5164.4,178", + pos="6752.4,178", width=3.8997]; "chemical gene interaction association" -> "anatomical context qualifier" [color=blue, label="anatomical context qualifier", - lp="5119.4,221.5", - pos="e,5107,194.48 2710.1,251.66 2733.5,249.77 2757.7,248.08 2780.4,247 3018.7,235.63 4690.2,254.75 4927.4,229 4985.4,222.71 5050,208.57 \ -5097.2,196.92", + lp="6709.4,221.5", + pos="e,6695.5,194.52 3433.9,251.63 3457.3,249.74 3481.6,248.06 3504.4,247 3838.8,231.45 6184.6,265.02 6517.4,229 6574.9,222.78 6639,208.63 \ +6685.8,196.97", style=solid]; subject [height=0.5, - pos="5367.4,178", + pos="6955.4,178", width=1.2277]; "chemical gene interaction association" -> subject [color=blue, label=subject, - lp="5306.4,221.5", - pos="e,5339.2,191.9 2709.9,251.66 2733.3,249.76 2757.6,248.08 2780.4,247 2916,240.6 5089.6,252.07 5223.4,229 5260.6,222.58 5301.1,207.79 \ -5329.6,195.95", + lp="6895.4,221.5", + pos="e,6927.3,192.03 3433.6,251.65 3457.1,249.74 3481.5,248.06 3504.4,247 3688,238.51 6632.3,260.46 6813.4,229 6850,222.64 6889.8,207.91 \ +6917.9,196.08", style=solid]; object [height=0.5, - pos="5410.4,91", + pos="6998.4,91", width=1.0832]; "chemical gene interaction association" -> object [color=blue, label=object, - lp="5461.4,178", - pos="e,5423.8,108.09 2709.9,251.65 2733.3,249.76 2757.6,248.07 2780.4,247 2922.2,240.33 5197,255.91 5336.4,229 5375.8,221.4 5394.1,226.25 \ -5420.4,196 5440.9,172.46 5442.3,156.9 5433.4,127 5432.4,123.55 5430.9,120.13 5429.1,116.85", + lp="7048.4,178", + pos="e,7011.8,108.09 3433.6,251.64 3457.1,249.74 3481.5,248.06 3504.4,247 3599.3,242.62 6832.1,247.12 6925.4,229 6964.4,221.43 6982.4,\ +225.99 7008.4,196 7028.8,172.42 7030.3,156.9 7021.4,127 7020.4,123.55 7018.9,120.13 7017.1,116.85", style=solid]; predicate [height=0.5, - pos="5564.4,178", + pos="7152.4,178", width=1.5165]; "chemical gene interaction association" -> predicate [color=blue, label=predicate, - lp="5537.4,221.5", - pos="e,5540.6,194.37 2709.9,251.65 2733.3,249.75 2757.6,248.07 2780.4,247 2854.8,243.51 5388.9,245.93 5461.4,229 5486.3,223.19 5512.2,\ -210.59 5531.8,199.5", + lp="7125.4,221.5", + pos="e,7128.6,194.39 3433.6,251.64 3457.1,249.74 3481.5,248.06 3504.4,247 3602.8,242.47 6953.5,251.31 7049.4,229 7074.3,223.21 7100.2,\ +210.61 7119.8,199.51", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2827.4,265", + pos="3551.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2958.4,265", + pos="3682.4,265", width=2.0762]; "chemical gene interaction association_subject form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="3309.4,265", + pos="4033.4,265", width=7.1855]; "chemical gene interaction association_subject part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="3834.4,265", + pos="4558.4,265", width=6.8966]; "chemical gene interaction association_subject derivative qualifier" [color=blue, height=0.5, label=ChemicalEntityDerivativeEnum, - pos="4258.4,265", + pos="4982.4,265", width=4.3871]; "chemical gene interaction association_subject context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="4526.4,265", + pos="5250.4,265", width=2.5456]; "chemical gene interaction association_object form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="4894.4,265", + pos="5618.4,265", width=7.1855]; "chemical gene interaction association_object part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="5419.4,265", + pos="6143.4,265", width=6.8966]; "chemical gene interaction association_object context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="5777.4,265", + pos="6501.4,265", width=2.5456]; "chemical gene interaction association_anatomical context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="5978.4,265", + pos="6702.4,265", width=2.5456]; subject -> object [label=relation, - lp="5405.4,134.5", - pos="e,5392.5,107.23 5368.5,159.55 5369.7,149.57 5372.2,137.07 5377.4,127 5379.6,122.68 5382.5,118.52 5385.7,114.66"]; + lp="6993.4,134.5", + pos="e,6980.5,107.23 6956.5,159.55 6957.7,149.57 6960.2,137.07 6965.4,127 6967.6,122.68 6970.5,118.52 6973.7,114.66"]; relation [height=0.5, - pos="5355.4,18", + pos="6943.4,18", width=1.2999]; - subject -> relation [pos="e,5356.7,36.188 5366.1,159.79 5364,132.48 5360,78.994 5357.5,46.38", + subject -> relation [pos="e,6944.7,36.188 6954.1,159.79 6952,132.48 6948,78.994 6945.5,46.38", style=dotted]; "chemical gene interaction association_subject" [color=blue, height=0.5, label="chemical entity", - pos="6170.4,265", + pos="6894.4,265", width=2.2748]; - object -> relation [pos="e,5368.2,35.54 5397.9,73.889 5391,64.939 5382.2,53.617 5374.4,43.584", + object -> relation [pos="e,6956.2,35.54 6985.9,73.889 6979,64.939 6970.2,53.617 6962.4,43.584", style=dotted]; "chemical gene interaction association_object" [color=blue, height=0.5, label="gene or gene product", - pos="6380.4,265", + pos="7104.4,265", width=3.0692]; "chemical gene interaction association_predicate" [color=blue, height=0.5, label="predicate type", - pos="6586.4,265", + pos="7310.4,265", width=2.1665]; } diff --git a/graphviz/chemical_gene_interaction_association.svg b/graphviz/chemical_gene_interaction_association.svg index 05bb366990..3df081f3a4 100644 --- a/graphviz/chemical_gene_interaction_association.svg +++ b/graphviz/chemical_gene_interaction_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical gene interaction association - -chemical gene interaction association + +chemical gene interaction association @@ -24,7 +24,7 @@ chemical gene interaction association->association - + is_a @@ -37,8 +37,8 @@ chemical gene interaction association->chemical to entity association mixin - - + + uses @@ -50,7 +50,7 @@ chemical gene interaction association->id - + id @@ -63,9 +63,9 @@ chemical gene interaction association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ chemical gene interaction association->name - - -name + + +name @@ -89,9 +89,9 @@ chemical gene interaction association->description - - -description + + +description @@ -102,9 +102,9 @@ chemical gene interaction association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ chemical gene interaction association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ chemical gene interaction association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ chemical gene interaction association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ chemical gene interaction association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ chemical gene interaction association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ chemical gene interaction association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ chemical gene interaction association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ chemical gene interaction association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ chemical gene interaction association->original subject - - -original subject + + +original subject @@ -232,9 +232,9 @@ chemical gene interaction association->original predicate - - -original predicate + + +original predicate @@ -245,281 +245,424 @@ chemical gene interaction association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical gene interaction association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical gene interaction association->object category + + +object category + + + +subject closure + +string + + + +chemical gene interaction association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical gene interaction association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical gene interaction association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical gene interaction association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical gene interaction association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical gene interaction association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical gene interaction association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical gene interaction association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical gene interaction association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical gene interaction association->type - - -type + + +type - + category - -category + +category - + chemical gene interaction association->category - - -category + + +category - + subject form or variant qualifier - -subject form or variant qualifier + +subject form or variant qualifier - + chemical gene interaction association->subject form or variant qualifier - - -subject form or variant qualifier + + +subject form or variant qualifier - + subject part qualifier - -subject part qualifier + +subject part qualifier - + chemical gene interaction association->subject part qualifier - - -subject part qualifier + + +subject part qualifier - + subject derivative qualifier - -subject derivative qualifier + +subject derivative qualifier - + chemical gene interaction association->subject derivative qualifier - - -subject derivative qualifier + + +subject derivative qualifier - + subject context qualifier - -subject context qualifier + +subject context qualifier - + chemical gene interaction association->subject context qualifier - - -subject context qualifier + + +subject context qualifier - + object form or variant qualifier - -object form or variant qualifier + +object form or variant qualifier - + chemical gene interaction association->object form or variant qualifier - - -object form or variant qualifier + + +object form or variant qualifier - + object part qualifier - -object part qualifier + +object part qualifier - + chemical gene interaction association->object part qualifier - - -object part qualifier + + +object part qualifier - + object context qualifier - -object context qualifier + +object context qualifier - + chemical gene interaction association->object context qualifier - - -object context qualifier + + +object context qualifier - + anatomical context qualifier - -anatomical context qualifier + +anatomical context qualifier - + chemical gene interaction association->anatomical context qualifier - - -anatomical context qualifier + + +anatomical context qualifier - + subject - -subject + +subject - + chemical gene interaction association->subject - - -subject + + +subject - + object - -object + +object - + chemical gene interaction association->object - - -object + + +object - + predicate - -predicate + +predicate - + chemical gene interaction association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + chemical gene interaction association_subject form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum - + chemical gene interaction association_subject part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum - + chemical gene interaction association_subject derivative qualifier - -ChemicalEntityDerivativeEnum + +ChemicalEntityDerivativeEnum - + chemical gene interaction association_subject context qualifier - -anatomical entity + +anatomical entity - + chemical gene interaction association_object form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum - + chemical gene interaction association_object part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum - + chemical gene interaction association_object context qualifier - -anatomical entity + +anatomical entity - + chemical gene interaction association_anatomical context qualifier - -anatomical entity + +anatomical entity - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + chemical gene interaction association_subject - -chemical entity + +chemical entity - + object->relation - - + + - + chemical gene interaction association_object - -gene or gene product + +gene or gene product - + chemical gene interaction association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv index 94ca2485c6..b536b5c966 100644 --- a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv +++ b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4916,283"]; + graph [bb="0,0,6632,283"]; node [label="\N"]; "chemical or drug or treatment side effect disease or phenotypic feature association" [height=0.5, label="chemical or drug or treatment side effect disease or phenotypic feature association", - pos="2883.4,265", + pos="3901.4,265", width=11.049]; "chemical or drug or treatment to disease or phenotypic feature association" [height=0.5, pos="359.42,178", width=9.9838]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "chemical or drug or treatment to disease or phenotypic feature association" [label=is_a, lp="1321.4,221.5", - pos="e,576.77,192.35 2509.2,258.9 2189.8,253.78 1718.3,244.4 1307.4,229 1061.1,219.77 778.97,204.26 586.99,192.95"]; + pos="e,571.57,192.57 3505,263.48 2996,261.69 2085.7,254.77 1307.4,229 1058.8,220.77 773.84,204.87 581.79,193.2"]; "chemical to entity association mixin" [height=0.5, pos="914.42,178", width=4.9287]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "chemical to entity association mixin" [label=uses, lp="1627.9,221.5", - pos="e,1039.4,190.81 2520.7,257.6 2266.2,252.23 1917.9,243.13 1611.4,229 1384.5,218.54 1327.9,213.62 1101.4,196 1084.6,194.69 1067,193.22 \ + pos="e,1039.4,190.81 3504.4,263.87 3047.6,262.34 2275,255.52 1611.4,229 1384.5,219.93 1327.9,213.62 1101.4,196 1084.6,194.69 1067,193.22 \ 1049.6,191.71"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="1384.4,178", width=7.6188]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, lp="1810.9,221.5", - pos="e,1490.8,194.61 2500.9,260.04 2291.9,255.78 2028.6,247.01 1794.4,229 1695.1,221.36 1582.8,207.28 1500.9,196.01"]; + pos="e,1488.2,194.7 3507.7,262.39 2992,259.42 2115.8,251.2 1794.4,229 1694,222.06 1580.4,207.69 1498.3,196.13"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> id [color=blue, label=id, - lp="1927.4,221.5", - pos="e,1744.4,189.97 2523.6,257.3 2299.8,251.89 2033.7,242.86 1920.4,229 1849.6,220.34 1832.1,215.28 1763.4,196 1760.3,195.13 1757.1,\ -194.16 1753.9,193.14", + lp="1928.4,221.5", + pos="e,1744.4,189.97 3513,261.06 2981.1,256.43 2074.3,246.16 1921.4,229 1850.1,221 1832.5,215.35 1763.4,196 1760.3,195.13 1757.1,194.16 \ +1753.9,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,8 @@ digraph { width=1.2277]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> iri [color=blue, label=iri, - lp="2031.4,221.5", - pos="e,1849.3,190.12 2539.4,255.95 2344.5,250.21 2120.8,241.32 2023.4,229 1954,220.21 1937.1,214.05 1869.4,196 1866,195.1 1862.6,194.12 \ -1859.1,193.09", + lp="2024.4,221.5", + pos="e,1849.6,190.01 3513.4,260.99 3004.8,256.39 2160.1,246.28 2016.4,229 1961.2,222.36 1899.4,205.37 1859.3,193.03", style=solid]; name [color=blue, height=0.5, @@ -53,8 +52,8 @@ digraph { width=1.5707]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> name [color=blue, label=name, - lp="2124.4,221.5", - pos="e,1970.8,192.2 2532.7,256.48 2366,251.23 2185.7,242.65 2104.4,229 2061.4,221.79 2014,207.12 1980.3,195.53", + lp="2120.4,221.5", + pos="e,1969.5,192.36 3508.9,262.08 3020.8,258.81 2235,250.28 2100.4,229 2058.4,222.35 2012.1,207.65 1979.3,195.9", style=solid]; description [color=blue, height=0.5, @@ -63,8 +62,8 @@ digraph { width=2.0943]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> description [color=blue, label=description, - lp="2225.9,221.5", - pos="e,2110.2,195.02 2509.4,258.86 2378,254.15 2247.6,245.34 2185.4,229 2162,222.86 2137.7,210.85 2118.9,200.14", + lp="2223.9,221.5", + pos="e,2109.6,195.24 3516.2,260.51 3029.4,255.46 2246.8,244.93 2183.4,229 2160.4,223.23 2136.7,211.31 2118.4,200.56", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +73,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="2342.4,221.5", - pos="e,2245.8,195.22 2576.8,253.53 2448.9,247.7 2323.5,239.48 2295.4,229 2279.8,223.17 2264.9,212.22 2253.3,202.06", + pos="e,2245.8,195.42 3510.4,261.57 3053.4,257.82 2351.8,248.87 2295.4,229 2279.7,223.46 2264.8,212.55 2253.2,202.32", style=solid]; subject [color=blue, height=0.5, @@ -84,7 +83,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> subject [color=blue, label=subject, lp="2436.4,221.5", - pos="e,2379.1,196.03 2602.2,252.25 2511.6,246.68 2429.4,239.02 2410.4,229 2400,223.5 2391.3,213.97 2384.8,204.7", + pos="e,2379,196.24 3506,262.96 3080.9,260.6 2458.9,253.03 2410.4,229 2399.7,223.71 2391,214.09 2384.4,204.68", style=solid]; object [color=blue, height=0.5, @@ -94,7 +93,8 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> object [color=blue, label=object, lp="2507.4,178", - pos="e,2465.8,109.02 2670.5,249.79 2590.7,240 2512.7,223.56 2485.4,196 2465.7,176.04 2463.5,142.62 2464.9,119.07", + pos="e,2465.7,109.09 3533.1,258.16 3241.3,252.61 2857.6,243.02 2702.4,229 2605.3,220.23 2554.8,264.6 2485.4,196 2465.5,176.25 2463.3,\ +142.8 2464.8,119.17", style=solid]; negated [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.2999]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2753.4,221.5", - pos="e,2616.5,191.48 2798.3,247.39 2774.3,242.12 2748.2,235.86 2724.4,229 2690.8,219.31 2653.6,205.77 2626.2,195.22", + lp="2812.4,221.5", + pos="e,2620,190.39 3519.3,259.98 3252.7,255.66 2920.9,246.84 2783.4,229 2729.6,222.02 2669.4,205.52 2629.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.1304]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2845.9,221.5", - pos="e,2752.9,195.02 2847.8,247.03 2836.4,241.45 2823.8,235.11 2812.4,229 2795.5,219.92 2777.1,209.3 2761.6,200.19", + lp="2945.9,221.5", + pos="e,2768.3,193.2 3523,259.45 3294.9,254.97 3026.9,246.18 2912.4,229 2866.1,222.05 2814.8,207.75 2777.9,196.22", style=solid]; publications [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=1.7332]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2927.4,221.5", - pos="e,2883.4,196.18 2883.4,246.8 2883.4,235.16 2883.4,219.55 2883.4,206.24", + lp="3083.4,221.5", + pos="e,2918,193.08 3528.2,258.73 3339.7,254.08 3131.7,245.35 3039.4,229 3000.8,222.15 2958.4,208.15 2927.6,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=2.0943]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="3044.9,221.5", - pos="e,3021.2,195.69 2936.2,247.01 2949.4,241.95 2963.2,235.88 2975.4,229 2988.8,221.48 3002.3,211.34 3013.5,202.15", + lp="3229.9,221.5", + pos="e,3073.9,194.09 3553,256.3 3406.6,251.14 3254,242.68 3183.4,229 3148.9,222.31 3111.4,209.1 3083.4,197.94", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -143,8 +143,8 @@ digraph { width=3.015]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="3208.9,221.5", - pos="e,3201.4,194.73 3003,247.83 3033.3,242.75 3065.8,236.47 3095.4,229 3128.1,220.77 3163.9,208.57 3191.8,198.28", + lp="3368.9,221.5", + pos="e,3257,195.95 3589.2,253.81 3459.7,248.06 3332.8,239.82 3304.4,229 3289.6,223.35 3275.6,212.89 3264.5,202.99", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -153,8 +153,8 @@ digraph { width=3.015]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3444.4,221.5", - pos="e,3426.2,193.96 3108.7,250.14 3164.1,245.05 3223.1,238.18 3277.4,229 3324.7,221.01 3377.3,207.6 3416.5,196.68", + lp="3535.4,221.5", + pos="e,3452.2,195.77 3574.4,254.73 3506.6,249.55 3452,241.49 3440.4,229 3433,220.97 3437.2,211.37 3445,202.74", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -163,8 +163,8 @@ digraph { width=3.015]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3710.9,221.5", - pos="e,3668.9,194.69 3164,252.21 3326.2,244.85 3505.5,235.55 3543.4,229 3583,222.17 3626.3,209.11 3659.1,198.05", + lp="3744.9,221.5", + pos="e,3662.2,194.17 3681.9,249.98 3662,244.87 3646.3,238.05 3638.4,229 3628,217.1 3637.8,206.69 3653.2,198.49", style=solid]; timepoint [color=blue, height=0.5, @@ -173,9 +173,8 @@ digraph { width=1.5346]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3886.4,221.5", - pos="e,3876.4,195.13 3161.2,252.11 3204.4,250.34 3248.6,248.58 3290.4,247 3349.4,244.77 3765.4,247.59 3821.4,229 3838.6,223.3 3855.4,\ -212.1 3868.4,201.75", + lp="3891.4,221.5", + pos="e,3870.6,194.47 3871.3,246.83 3865.3,241.89 3859.8,235.93 3856.4,229 3851.7,219.42 3856.2,209.79 3863.4,201.57", style=solid]; "original subject" [color=blue, height=0.5, @@ -184,9 +183,8 @@ digraph { width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="4014.4,221.5", - pos="e,3987.4,194.2 3158.7,252 3202.8,250.22 3247.8,248.49 3290.4,247 3361,244.53 3857.9,249.42 3925.4,229 3944.9,223.1 3964.4,211.1 \ -3979.2,200.34", + lp="4005.4,221.5", + pos="e,3981.4,192.24 3916,246.75 3925.1,236.6 3937.3,223.86 3949.4,214 3956.6,208.17 3964.8,202.54 3972.7,197.56", style=solid]; "original predicate" [color=blue, height=0.5, @@ -195,58 +193,174 @@ digraph { width=1.5887]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="4158.9,221.5", - pos="e,4109.6,195.8 3156.2,251.9 3201.1,250.11 3247,248.4 3290.4,247 3334,245.59 4034.8,247.18 4074.4,229 4086.1,223.65 4096,213.69 4103.6,\ -204.05", + lp="4147.9,221.5", + pos="e,4104.3,195.85 4011.1,247.63 4028.4,242.9 4045.8,236.82 4061.4,229 4074.5,222.46 4087,212.32 4097.1,202.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="4251.4,178", + pos="4233.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="4291.9,221.5", - pos="e,4247.7,196.03 3154.6,251.82 3199.9,250.03 3246.5,248.34 3290.4,247 3316.4,246.21 4204.4,242.88 4226.4,229 4234.9,223.67 4240.5,\ -214.56 4244.3,205.56", + lp="4275.9,221.5", + pos="e,4230.4,196.13 4145.7,250.74 4174.5,245.61 4198.4,238.59 4211.4,229 4219.1,223.36 4224.1,214.47 4227.4,205.74", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="4366.4,178", + width=2.1304]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="4406.9,221.5", + pos="e,4359.3,195.95 4164.2,251.47 4243.9,245.91 4314.9,238.45 4331.4,229 4341.1,223.47 4348.7,214.06 4354.3,204.89", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="4537.4,178", + width=2.1304]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="4552.9,221.5", + pos="e,4520.9,195.7 4160.6,251.34 4303.4,243.8 4455,234.64 4470.4,229 4486.1,223.24 4501.3,212.51 4513.2,202.47", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4670.4,178", + width=1.0652]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="4688.9,221.5", + pos="e,4654.7,194.68 4182.2,252.25 4376.5,243.78 4602,233.15 4612.4,229 4620.3,225.85 4634.7,213.43 4647.2,201.76", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4766.4,178", + width=1.0652]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4807.4,221.5", + pos="e,4763.9,196.35 4182.2,252.25 4224.5,250.49 4267.6,248.69 4308.4,247 4332.7,245.99 4725.5,242.86 4745.4,229 4753.2,223.61 4758.1,\ +214.78 4761.2,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4899.4,178", + width=2.1304]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4965.9,221.5", + pos="e,4891.4,196.18 4178.6,252.08 4222.1,250.31 4266.5,248.56 4308.4,247 4339.1,245.86 4834.1,243.11 4861.4,229 4871.7,223.69 4880,214.2 \ +4886.2,204.89", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="5088.4,178", + width=2.1304]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="5155.9,221.5", + pos="e,5082.7,196.12 4174.8,251.92 4219.4,250.13 4265.2,248.42 4308.4,247 4350,245.63 5021.3,249.68 5057.4,229 5066.6,223.73 5073.5,214.5 \ +5078.3,205.39", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="5278.4,178", + width=1.0652]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="5328.4,221.5", + pos="e,5271.4,196.2 4172.6,251.82 4217.9,250.03 4264.5,248.34 4308.4,247 4334.4,246.21 5220.5,241.22 5243.4,229 5253.2,223.77 5260.9,\ +214.42 5266.5,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="5437.4,178", + width=1.0652]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="5481.4,221.5", + pos="e,5430.1,195.74 4171.2,251.77 4217,249.97 4264.1,248.29 4308.4,247 4338.7,246.12 5373.4,242.88 5400.4,229 5410.8,223.68 5418.9,214 \ +5425,204.57", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="5588.4,178", + width=1.0652]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5641.4,221.5", + pos="e,5580.4,195.77 4170.4,251.73 4216.4,249.93 4263.8,248.26 4308.4,247 4342.9,246.03 5518.5,244.35 5549.4,229 5560.1,223.67 5568.8,\ +213.85 5575.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5759.4,178", + width=1.0652]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5806.9,221.5", + pos="e,5751.1,195.79 4169.6,251.69 4215.9,249.89 4263.5,248.22 4308.4,247 4347.6,245.93 5684.2,246.2 5719.4,229 5730.3,223.7 5739.1,213.88 \ +5745.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5921.4,178", + width=2.347]; + "chemical or drug or treatment side effect disease or phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5969.9,221.5", + pos="e,5912.5,196.3 4169,251.67 4215.5,249.86 4263.3,248.2 4308.4,247 4352.1,245.84 5841.1,247.9 5880.4,229 5891.3,223.79 5900.2,214.18 \ +5907,204.76", style=solid]; type [height=0.5, - pos="4339.4,178", + pos="6055.4,178", width=0.86659]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> type [color=blue, label=type, - lp="4369.4,221.5", - pos="e,4348.4,195.56 3153.5,251.78 3199.2,249.98 3246.1,248.3 3290.4,247 3319.8,246.14 4326.8,249.94 4347.4,229 4353.5,222.78 4353.7,\ -213.88 4351.6,205.3", + lp="6069.4,221.5", + pos="e,6056.3,196.18 4168.5,251.65 4215.1,249.83 4263.2,248.18 4308.4,247 4332.5,246.37 6024.6,244.02 6043.4,229 6050.3,223.54 6053.6,\ +214.92 6055.2,206.37", style=solid]; category [height=0.5, - pos="4440.4,178", + pos="6156.4,178", width=1.4263]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> category [color=blue, label=category, - lp="4443.9,221.5", - pos="e,4428.7,195.87 3153.2,251.77 3199,249.97 3246.1,248.29 3290.4,247 3351.5,245.23 4333.1,252.55 4389.4,229 4402.2,223.64 4413.6,213.4 \ -4422.3,203.57", + lp="6149.9,221.5", + pos="e,6140.8,195.25 4168.2,251.65 4214.9,249.83 4263.1,248.18 4308.4,247 4357.9,245.72 6042.5,244.83 6089.4,229 6105.6,223.53 6121.1,\ +212.51 6133.1,202.2", style=solid]; "FDA adverse event level" [color=blue, height=0.5, label=FDAIDAAdverseEventEnum, - pos="4649.4,178", + pos="6365.4,178", width=3.8816]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "FDA adverse event level" [color=blue, label="FDA adverse event level", - lp="4633.9,221.5", - pos="e,4606.5,195.15 3152.7,251.74 3198.6,249.94 3245.9,248.27 3290.4,247 3422.5,243.24 4348.8,248.82 4479.4,229 4519.7,222.89 4563.8,\ -209.72 4597,198.43", + lp="6343.9,221.5", + pos="e,6320.2,195.09 4168.2,251.63 4214.9,249.81 4263.1,248.16 4308.4,247 4516.9,241.65 5978.9,258.16 6185.4,229 6228.3,222.95 6275.4,\ +209.62 6310.6,198.24", style=solid]; predicate [height=0.5, - pos="4861.4,178", + pos="6577.4,178", width=1.5165]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="4812.4,221.5", - pos="e,4831.7,193.26 3151.6,251.69 3197.9,249.88 3245.5,248.22 3290.4,247 3370.1,244.84 4647,243.46 4725.4,229 4759.2,222.76 4795.7,208.93 \ -4822.4,197.39", + lp="6524.4,221.5", + pos="e,6546.9,193.06 4167.6,251.61 4214.5,249.79 4262.9,248.14 4308.4,247 4426.6,244.03 6319,249.4 6435.4,229 6471,222.76 6509.5,208.69 \ +6537.5,197.06", style=solid]; subject -> object [label=relation, lp="2434.4,134.5", @@ -261,16 +375,16 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3337.4,265", + pos="4355.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3468.4,265", + pos="4486.4,265", width=2.0762]; "chemical or drug or treatment side effect disease or phenotypic feature association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3639.4,265", + pos="4657.4,265", width=2.1665]; } diff --git a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg index 5a9bb1a07d..095e1c57ea 100644 --- a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg +++ b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical or drug or treatment side effect disease or phenotypic feature association - -chemical or drug or treatment side effect disease or phenotypic feature association + +chemical or drug or treatment side effect disease or phenotypic feature association @@ -24,8 +24,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->chemical or drug or treatment to disease or phenotypic feature association - - + + is_a @@ -37,7 +37,7 @@ chemical or drug or treatment side effect disease or phenotypic feature association->chemical to entity association mixin - + uses @@ -50,8 +50,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - + + uses @@ -63,9 +63,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->description - - -description + + +description @@ -115,8 +115,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->subject - - + + subject @@ -141,8 +141,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->object - - + + object @@ -154,9 +154,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -258,9 +258,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->original subject - - -original subject + + +original subject @@ -271,117 +271,260 @@ chemical or drug or treatment side effect disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical or drug or treatment side effect disease or phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical or drug or treatment side effect disease or phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +chemical or drug or treatment side effect disease or phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical or drug or treatment side effect disease or phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical or drug or treatment side effect disease or phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical or drug or treatment side effect disease or phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical or drug or treatment side effect disease or phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical or drug or treatment side effect disease or phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical or drug or treatment side effect disease or phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical or drug or treatment side effect disease or phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical or drug or treatment side effect disease or phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical or drug or treatment side effect disease or phenotypic feature association->type - - -type + + +type - + category - -category + +category - + chemical or drug or treatment side effect disease or phenotypic feature association->category - - -category + + +category - + FDA adverse event level - -FDAIDAAdverseEventEnum + +FDAIDAAdverseEventEnum - + chemical or drug or treatment side effect disease or phenotypic feature association->FDA adverse event level - - -FDA adverse event level + + +FDA adverse event level - + predicate - -predicate + +predicate - + chemical or drug or treatment side effect disease or phenotypic feature association->predicate - - -predicate + + +predicate - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type - + chemical or drug or treatment side effect disease or phenotypic feature association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv index c26dd5ff31..1cd6b7a62a 100644 --- a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv @@ -1,30 +1,30 @@ digraph { - graph [bb="0,0,4322,283"]; + graph [bb="0,0,6038,283"]; node [label="\N"]; "chemical or drug or treatment to disease or phenotypic feature association" [height=0.5, label="chemical or drug or treatment to disease or phenotypic feature association", - pos="2289.4,265", + pos="3307.4,265", width=9.9838]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical or drug or treatment to disease or phenotypic feature association" -> association [label=is_a, lp="727.39,221.5", - pos="e,106.71,190.75 1945,259.79 1625.6,255.07 1137.3,245.78 713.39,229 455.85,218.8 389.46,233.09 134.39,196 128.61,195.16 122.61,194.08 \ + pos="e,106.71,190.75 2948.2,264.08 2447.5,263.07 1511.1,257.1 713.39,229 455.8,219.93 389.46,233.09 134.39,196 128.61,195.16 122.61,194.08 \ 116.66,192.88"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical or drug or treatment to disease or phenotypic feature association" -> "chemical to entity association mixin" [label=uses, lp="1033.9,221.5", - pos="e,445.34,190.81 1956.2,258.21 1699.5,252.93 1335.9,243.68 1017.4,229 790.49,218.54 733.85,213.62 507.39,196 490.62,194.69 473,193.22 \ + pos="e,445.34,190.81 2948.3,263.98 2497.3,262.71 1699.8,256.27 1017.4,229 790.44,219.93 733.85,213.62 507.39,196 490.62,194.69 473,193.22 \ 455.57,191.71"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="790.39,178", width=7.6188]; "chemical or drug or treatment to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, lp="1216.9,221.5", - pos="e,896.75,194.61 1940.1,260.69 1726.3,256.7 1447.2,247.98 1200.4,229 1101,221.36 988.75,207.28 906.84,196.01"]; + pos="e,894.16,194.7 2951.1,262.6 2441.5,259.82 1529.7,251.75 1200.4,229 1100,222.06 986.37,207.69 904.27,196.13"]; id [color=blue, height=0.5, label=string, @@ -32,8 +32,8 @@ digraph { width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> id [color=blue, label=id, - lp="1333.4,221.5", - pos="e,1150.4,189.97 1958.2,257.98 1728.9,252.66 1444.6,243.46 1326.4,229 1255.6,220.34 1238,215.28 1169.4,196 1166.3,195.13 1163.1,194.16 \ + lp="1334.4,221.5", + pos="e,1150.4,189.97 2955.1,261.37 2429.3,256.9 1483.8,246.56 1327.4,229 1256.1,221 1238.5,215.35 1169.4,196 1166.3,195.13 1163.1,194.16 \ 1159.9,193.14", style=solid]; iri [color=blue, @@ -43,9 +43,8 @@ digraph { width=1.2277]; "chemical or drug or treatment to disease or phenotypic feature association" -> iri [color=blue, label=iri, - lp="1437.4,221.5", - pos="e,1255.3,190.12 1970.5,256.67 1770.1,250.97 1530.9,241.85 1429.4,229 1360,220.21 1343,214.05 1275.4,196 1272,195.1 1268.6,194.12 \ -1265.1,193.09", + lp="1430.4,221.5", + pos="e,1255.5,190.01 2955.5,261.31 2451.8,256.87 1569.5,246.7 1422.4,229 1367.2,222.36 1305.3,205.37 1265.2,193.03", style=solid]; name [color=blue, height=0.5, @@ -54,8 +53,8 @@ digraph { width=1.5707]; "chemical or drug or treatment to disease or phenotypic feature association" -> name [color=blue, label=name, - lp="1530.4,221.5", - pos="e,1376.7,192.2 1964.5,257.27 1791,252.11 1595.9,243.35 1510.4,229 1467.4,221.79 1419.9,207.12 1386.3,195.53", + lp="1526.4,221.5", + pos="e,1375.5,192.36 2951.8,262.32 2467.5,259.23 1644.4,250.82 1506.4,229 1464.3,222.35 1418.1,207.65 1385.2,195.9", style=solid]; description [color=blue, height=0.5, @@ -64,8 +63,8 @@ digraph { width=2.0943]; "chemical or drug or treatment to disease or phenotypic feature association" -> description [color=blue, label=description, - lp="1631.9,221.5", - pos="e,1516.1,195.02 1944.6,259.84 1803.7,255.41 1658.2,246.55 1591.4,229 1568,222.86 1543.7,210.85 1524.9,200.14", + lp="1629.9,221.5", + pos="e,1515.5,195.24 2957.5,260.87 2474.3,255.97 1654.4,245.32 1589.4,229 1566.4,223.23 1542.7,211.31 1524.3,200.56", style=solid]; "has attribute" [color=blue, height=0.5, @@ -75,7 +74,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1748.4,221.5", - pos="e,1651.8,195.22 2000,254.3 1866.4,248.43 1730.7,239.95 1701.4,229 1685.8,223.17 1670.9,212.22 1659.3,202.06", + pos="e,1651.7,195.42 2953.3,261.87 2498.2,258.3 1759.3,249.41 1701.4,229 1685.7,223.46 1670.8,212.55 1659.2,202.32", style=solid]; subject [color=blue, height=0.5, @@ -85,7 +84,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> subject [color=blue, label=subject, lp="1842.4,221.5", - pos="e,1785.1,196.03 2020.9,253.02 1925.3,247.39 1836.3,239.48 1816.4,229 1806,223.5 1797.3,213.97 1790.7,204.7", + pos="e,1785,196.24 2949.6,263.16 2524.6,261.04 1866.4,253.75 1816.4,229 1805.7,223.71 1797,214.09 1790.4,204.68", style=solid]; object [color=blue, height=0.5, @@ -95,7 +94,8 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> object [color=blue, label=object, lp="1913.4,178", - pos="e,1871.7,109.02 2080.8,250.31 1999.5,240.6 1919.2,224.06 1891.4,196 1871.6,176.04 1869.5,142.62 1870.9,119.07", + pos="e,1871.7,109.09 2970.2,258.74 2675.1,253.29 2269.2,243.52 2108.4,229 2011.2,220.23 1960.8,264.6 1891.4,196 1871.4,176.25 1869.3,\ +142.8 1870.8,119.17", style=solid]; negated [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { width=1.2999]; "chemical or drug or treatment to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2159.4,221.5", - pos="e,2022.5,191.48 2204.7,247.48 2180.5,242.19 2154.3,235.9 2130.4,229 2096.8,219.31 2059.6,205.77 2032.1,195.22", + lp="2218.4,221.5", + pos="e,2026,190.39 2959.2,260.52 2687.5,256.41 2332.7,247.6 2189.4,229 2135.6,222.02 2075.4,205.52 2035.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=2.1304]; "chemical or drug or treatment to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2251.9,221.5", - pos="e,2158.9,195.02 2253.8,247.03 2242.4,241.45 2229.8,235.11 2218.4,229 2201.5,219.92 2183,209.3 2167.6,200.19", + lp="2351.9,221.5", + pos="e,2174.3,193.2 2961.7,260.06 2727.1,255.8 2438.4,247.01 2318.4,229 2272.1,222.05 2220.8,207.75 2183.8,196.22", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=1.7332]; "chemical or drug or treatment to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2333.4,221.5", - pos="e,2289.4,196.18 2289.4,246.8 2289.4,235.16 2289.4,219.55 2289.4,206.24", + lp="2489.4,221.5", + pos="e,2324,193.08 2965.4,259.47 2769.1,255.02 2542.8,246.26 2445.4,229 2406.7,222.15 2364.4,208.15 2333.6,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=2.0943]; "chemical or drug or treatment to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2450.9,221.5", - pos="e,2427.1,195.69 2342.2,247.01 2355.4,241.95 2369.2,235.88 2381.4,229 2394.7,221.48 2408.3,211.34 2419.5,202.15", + lp="2635.9,221.5", + pos="e,2479.8,194.09 2983.7,257.15 2830,252.08 2664,243.46 2589.4,229 2554.9,222.31 2517.4,209.1 2489.3,197.94", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -144,8 +144,8 @@ digraph { width=3.015]; "chemical or drug or treatment to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2614.9,221.5", - pos="e,2607.3,194.73 2408.1,247.97 2438.7,242.86 2471.5,236.54 2501.4,229 2534,220.77 2569.8,208.57 2597.8,198.28", + lp="2774.9,221.5", + pos="e,2663,195.95 3013.5,254.61 2877.8,248.83 2740.1,240.33 2710.4,229 2695.6,223.35 2681.5,212.89 2670.5,202.99", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -154,8 +154,8 @@ digraph { width=3.015]; "chemical or drug or treatment to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2850.4,221.5", - pos="e,2832.1,193.96 2508.5,250.71 2565.6,245.56 2627,238.52 2683.4,229 2730.7,221.01 2783.2,207.6 2822.5,196.68", + lp="2941.4,221.5", + pos="e,2858.2,195.77 2996.7,255.92 2921.5,250.8 2858.9,242.48 2846.4,229 2839,220.97 2843.2,211.37 2851,202.74", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -164,8 +164,8 @@ digraph { width=3.015]; "chemical or drug or treatment to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3116.9,221.5", - pos="e,3074.9,194.69 2540.2,252.08 2718.1,243.39 2928.8,232.56 2949.4,229 2988.9,222.17 3032.3,209.11 3065.1,198.05", + lp="3150.9,221.5", + pos="e,3068.2,194.17 3090.4,250.63 3069.3,245.45 3052.7,238.44 3044.4,229 3034,217.1 3043.7,206.69 3059.1,198.49", style=solid]; timepoint [color=blue, height=0.5, @@ -174,9 +174,8 @@ digraph { width=1.5346]; "chemical or drug or treatment to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3292.4,221.5", - pos="e,3282.3,195.14 2539,252.01 2578.9,250.24 2619.8,248.5 2658.4,247 2721.6,244.54 3167.3,248.86 3227.4,229 3244.6,223.32 3261.3,212.12 \ -3274.4,201.76", + lp="3297.4,221.5", + pos="e,3276.6,194.47 3277.3,246.83 3271.3,241.89 3265.8,235.93 3262.4,229 3257.7,219.42 3262.1,209.79 3269.4,201.57", style=solid]; "original subject" [color=blue, height=0.5, @@ -185,9 +184,8 @@ digraph { width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3420.4,221.5", - pos="e,3393.7,193.97 2537,251.93 2577.5,250.15 2619.1,248.43 2658.4,247 2733.1,244.28 3259.8,250.58 3331.4,229 3351.1,223.07 3370.7,210.96 \ -3385.5,200.14", + lp="3411.4,221.5", + pos="e,3387.4,192.24 3322,246.75 3331.1,236.6 3343.3,223.86 3355.4,214 3362.6,208.17 3370.8,202.54 3378.7,197.56", style=solid]; "original predicate" [color=blue, height=0.5, @@ -196,58 +194,174 @@ digraph { width=1.5887]; "chemical or drug or treatment to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3564.9,221.5", - pos="e,3515.5,195.8 2535,251.86 2576.2,250.06 2618.5,248.36 2658.4,247 2704,245.45 3438.9,248.04 3480.4,229 3492.1,223.65 3502,213.69 \ -3509.5,204.06", + lp="3553.9,221.5", + pos="e,3510.2,195.85 3416.6,247.74 3434.1,243 3451.6,236.88 3467.4,229 3480.5,222.46 3493,212.32 3503.1,202.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3657.4,178", + pos="3639.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3697.9,221.5", - pos="e,3653.7,196.03 2534,251.78 2575.5,249.98 2618.2,248.3 2658.4,247 2685.4,246.13 3609.5,243.44 3632.4,229 3640.8,223.68 3646.5,214.56 \ -3650.3,205.56", + lp="3681.9,221.5", + pos="e,3636.4,196.13 3546.9,251.56 3577.9,246.37 3603.7,239.11 3617.4,229 3625.1,223.36 3630.1,214.47 3633.4,205.74", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3772.4,178", + width=2.1304]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3812.9,221.5", + pos="e,3765.3,195.95 3559.8,252.18 3643.7,246.55 3720.2,238.86 3737.4,229 3747,223.47 3754.7,214.06 3760.3,204.89", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3943.4,178", + width=2.1304]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3958.9,221.5", + pos="e,3926.9,195.7 3555.2,251.93 3701.3,244.29 3860.6,234.78 3876.4,229 3892.1,223.24 3907.3,212.51 3919.2,202.47", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4076.4,178", + width=1.0652]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="4094.9,221.5", + pos="e,4060.6,194.68 3558.7,252.09 3762.2,242.38 4015.7,230.1 4018.4,229 4026.3,225.85 4040.7,213.43 4053.2,201.76", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4172.4,178", + width=1.0652]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4213.4,221.5", + pos="e,4169.9,196.36 3559,252.13 3598.3,250.36 3638.4,248.59 3676.4,247 3702.8,245.89 4129.7,244.03 4151.4,229 4159.2,223.63 4164.1,214.79 \ +4167.2,206.03", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4305.4,178", + width=2.1304]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4371.9,221.5", + pos="e,4297.4,196.19 3556.5,251.99 3596.6,250.22 3637.6,248.48 3676.4,247 3709.2,245.74 4238.2,244.04 4267.4,229 4277.7,223.7 4286,214.21 \ +4292.1,204.91", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4494.4,178", + width=2.1304]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4561.9,221.5", + pos="e,4488.7,196.12 3553.5,251.87 3594.5,250.07 3636.7,248.37 3676.4,247 3720.1,245.49 4425.4,250.71 4463.4,229 4472.6,223.73 4479.4,\ +214.5 4484.3,205.4", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4684.4,178", + width=1.0652]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4734.4,221.5", + pos="e,4677.4,196.2 3552,251.78 3593.5,249.98 3636.2,248.3 3676.4,247 3703.4,246.13 4625.5,241.71 4649.4,229 4659.2,223.77 4666.9,214.42 \ +4672.5,205.21", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4843.4,178", + width=1.0652]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4887.4,221.5", + pos="e,4836,195.74 3551,251.74 3592.8,249.93 3635.9,248.26 3676.4,247 3707.8,246.03 4778.5,243.35 4806.4,229 4816.7,223.69 4824.9,214.01 \ +4830.9,204.57", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4994.4,178", + width=1.0652]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5047.4,221.5", + pos="e,4986.4,195.78 3550,251.72 3592.1,249.9 3635.5,248.23 3676.4,247 3711.9,245.93 4923.6,244.81 4955.4,229 4966.1,223.67 4974.8,213.85 \ +4981.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5165.4,178", + width=1.0652]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5212.9,221.5", + pos="e,5157.1,195.79 3549.5,251.68 3591.8,249.86 3635.4,248.2 3676.4,247 3716.6,245.82 5089.2,246.66 5125.4,229 5136.3,223.7 5145.1,213.88 \ +5151.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5327.4,178", + width=2.347]; + "chemical or drug or treatment to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5375.9,221.5", + pos="e,5318.5,196.31 3549,251.66 3591.5,249.84 3635.2,248.18 3676.4,247 3721.1,245.72 5246.1,248.36 5286.4,229 5297.2,223.79 5306.2,214.18 \ +5312.9,204.76", style=solid]; type [height=0.5, - pos="3745.4,178", + pos="5461.4,178", width=0.86659]; "chemical or drug or treatment to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="3775.4,221.5", - pos="e,3754.3,195.56 2533,251.76 2574.8,249.95 2617.9,248.27 2658.4,247 2688.8,246.05 3732.1,250.69 3753.4,229 3759.5,222.78 3759.7,213.88 \ -3757.6,205.3", + lp="5475.4,221.5", + pos="e,5462.2,196.18 3548.5,251.64 3591.1,249.82 3635,248.16 3676.4,247 3701,246.31 5430.1,244.34 5449.4,229 5456.2,223.54 5459.6,214.92 \ +5461.1,206.37", style=solid]; category [height=0.5, - pos="3846.4,178", + pos="5562.4,178", width=1.4263]; "chemical or drug or treatment to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="3849.9,221.5", - pos="e,3834.7,195.88 2533,251.73 2574.8,249.93 2617.9,248.25 2658.4,247 2721.5,245.05 3737.1,253.35 3795.4,229 3808.2,223.65 3819.6,213.4 \ -3828.3,203.57", + lp="5555.9,221.5", + pos="e,5546.8,195.25 3548.5,251.64 3591.1,249.81 3635,248.16 3676.4,247 3726.9,245.59 5447.5,245.16 5495.4,229 5511.6,223.53 5527.1,212.51 \ +5539.1,202.2", style=solid]; "FDA adverse event level" [color=blue, height=0.5, label=FDAIDAAdverseEventEnum, - pos="4055.4,178", + pos="5771.4,178", width=3.8816]; "chemical or drug or treatment to disease or phenotypic feature association" -> "FDA adverse event level" [color=blue, label="FDA adverse event level", - lp="4039.9,221.5", - pos="e,4012.5,195.16 2532.5,251.72 2574.5,249.9 2617.7,248.24 2658.4,247 2794.7,242.86 3750.6,249.42 3885.4,229 3925.7,222.9 3969.8,209.73 \ -4003,198.44", + lp="5749.9,221.5", + pos="e,5726.2,195.1 3548.5,251.62 3591.1,249.79 3635,248.15 3676.4,247 3889.1,241.1 5380.7,258.73 5591.4,229 5634.3,222.95 5681.3,209.62 \ +5716.6,198.25", style=solid]; predicate [height=0.5, - pos="4267.4,178", + pos="5983.4,178", width=1.5165]; "chemical or drug or treatment to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="4218.4,221.5", - pos="e,4237.7,193.26 2531.5,251.67 2573.8,249.86 2617.4,248.2 2658.4,247 2740.2,244.62 4050.9,243.83 4131.4,229 4165.2,222.77 4201.7,\ -208.93 4228.4,197.39", + lp="5930.4,221.5", + pos="e,5952.9,193.06 3548,251.6 3590.8,249.77 3634.9,248.13 3676.4,247 3796.6,243.73 5722.9,249.76 5841.4,229 5877,222.77 5915.5,208.69 \ +5943.5,197.06", style=solid]; subject -> object [label=relation, lp="1840.4,134.5", @@ -262,16 +376,16 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2705.4,265", + pos="3723.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2836.4,265", + pos="3854.4,265", width=2.0762]; "chemical or drug or treatment to disease or phenotypic feature association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3007.4,265", + pos="4025.4,265", width=2.1665]; } diff --git a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg index f6358d5a10..48913aacac 100644 --- a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical or drug or treatment to disease or phenotypic feature association - -chemical or drug or treatment to disease or phenotypic feature association + +chemical or drug or treatment to disease or phenotypic feature association @@ -24,7 +24,7 @@ chemical or drug or treatment to disease or phenotypic feature association->association - + is_a @@ -37,7 +37,7 @@ chemical or drug or treatment to disease or phenotypic feature association->chemical to entity association mixin - + uses @@ -50,8 +50,8 @@ chemical or drug or treatment to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - + + uses @@ -63,9 +63,9 @@ chemical or drug or treatment to disease or phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ chemical or drug or treatment to disease or phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ chemical or drug or treatment to disease or phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ chemical or drug or treatment to disease or phenotypic feature association->description - - -description + + +description @@ -115,8 +115,8 @@ chemical or drug or treatment to disease or phenotypic feature association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ chemical or drug or treatment to disease or phenotypic feature association->subject - - + + subject @@ -141,8 +141,8 @@ chemical or drug or treatment to disease or phenotypic feature association->object - - + + object @@ -154,9 +154,9 @@ chemical or drug or treatment to disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ chemical or drug or treatment to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ chemical or drug or treatment to disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ chemical or drug or treatment to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ chemical or drug or treatment to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ chemical or drug or treatment to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ chemical or drug or treatment to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ chemical or drug or treatment to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -258,9 +258,9 @@ chemical or drug or treatment to disease or phenotypic feature association->original subject - - -original subject + + +original subject @@ -271,117 +271,260 @@ chemical or drug or treatment to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical or drug or treatment to disease or phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical or drug or treatment to disease or phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical or drug or treatment to disease or phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +chemical or drug or treatment to disease or phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical or drug or treatment to disease or phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical or drug or treatment to disease or phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical or drug or treatment to disease or phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical or drug or treatment to disease or phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical or drug or treatment to disease or phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical or drug or treatment to disease or phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical or drug or treatment to disease or phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical or drug or treatment to disease or phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical or drug or treatment to disease or phenotypic feature association->type - - -type + + +type - + category - -category + +category - + chemical or drug or treatment to disease or phenotypic feature association->category - - -category + + +category - + FDA adverse event level - -FDAIDAAdverseEventEnum + +FDAIDAAdverseEventEnum - + chemical or drug or treatment to disease or phenotypic feature association->FDA adverse event level - - -FDA adverse event level + + +FDA adverse event level - + predicate - -predicate + +predicate - + chemical or drug or treatment to disease or phenotypic feature association->predicate - - -predicate + + +predicate - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type - + chemical or drug or treatment to disease or phenotypic feature association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_to_chemical_association.gv b/graphviz/chemical_to_chemical_association.gv index e5c4e7e8e3..a563126ed6 100644 --- a/graphviz/chemical_to_chemical_association.gv +++ b/graphviz/chemical_to_chemical_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3487.4,283"]; + graph [bb="0,0,5202.4,283"]; node [label="\N"]; "chemical to chemical association" [height=0.5, label="chemical to chemical association", - pos="1816.4,265", + pos="2834.4,265", width=4.5135]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical to chemical association" -> association [label=is_a, - lp="506.39,221.5", - pos="e,107.14,190.59 1654.7,263.13 1405.1,261.03 911.02,253.8 492.39,229 332.89,219.55 292.09,221.76 134.39,196 128.71,195.07 122.81,\ -193.95 116.94,192.72"]; + lp="496.39,221.5", + pos="e,107.14,190.57 2672.5,263.27 2213.5,260.94 909.66,252.4 482.39,229 327.27,220.5 287.69,221.24 134.39,196 128.71,195.06 122.81,193.93 \ +116.94,192.71"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical to chemical association" -> "chemical to entity association mixin" [label=uses, - lp="654.89,221.5", - pos="e,398.78,194.15 1656.4,261.75 1381.6,257.47 830.98,246.93 638.39,229 560.35,221.73 472.38,207.42 408.78,195.97"]; + lp="652.89,221.5", + pos="e,397.29,194.28 2671.7,264.39 2232.8,264.95 1031.3,263.22 636.39,229 558.39,222.24 470.48,207.77 407.23,196.12"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "chemical to chemical association" -> id [color=blue, label=id, - lp="778.39,221.5", - pos="e,583.11,189.95 1656.3,261.76 1407.1,257.74 937.78,247.91 771.39,229 695.35,220.36 676.22,216.16 602.39,196 599.24,195.14 595.99,\ -194.17 592.75,193.15", + lp="773.39,221.5", + pos="e,583.37,190.01 2672.6,262.95 2218.5,259.78 953.32,249.22 766.39,229 692.48,221 674.06,215.79 602.39,196 599.28,195.14 596.08,194.18 \ +592.89,193.17", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "chemical to chemical association" -> iri [color=blue, label=iri, - lp="904.39,221.5", - pos="e,687.99,190.23 1653.9,264.47 1469.7,263.45 1160.6,257.09 896.39,229 812.04,220.03 790.75,216.34 708.39,196 704.96,195.15 701.42,\ -194.2 697.89,193.19", + lp="891.39,221.5", + pos="e,688.01,190.16 2671.9,264.61 2268.3,265.55 1228.2,264.35 883.39,229 804.66,220.93 785.11,215.46 708.39,196 704.97,195.13 701.43,\ +194.16 697.9,193.14", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "chemical to chemical association" -> name [color=blue, label=name, - lp="1016.4,221.5", - pos="e,814.9,190.59 1659.2,260.39 1457.9,255.24 1120.1,244.61 996.39,229 936.63,221.46 869.31,205.16 824.63,193.22", + lp="1005.4,221.5", + pos="e,813.59,191.06 2673,262.84 2253.4,259.55 1150,249.08 985.39,229 929,222.12 865.78,205.98 823.37,193.88", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "chemical to chemical association" -> description [color=blue, label=description, - lp="1145.9,221.5", - pos="e,965.52,193.16 1659.2,260.3 1482.9,255.43 1208,245.5 1105.4,229 1060.7,221.81 1011.2,207.7 975.27,196.29", + lp="1136.9,221.5", + pos="e,963.36,193.52 2672.4,263.16 2270.6,260.74 1249.2,252.33 1096.4,229 1053.9,222.51 1007.1,208.43 973.04,196.86", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "chemical to chemical association" -> "has attribute" [color=blue, label="has attribute", - lp="1305.4,221.5", - pos="e,1105.9,191.01 1656.2,261.99 1544.2,258.63 1391.4,250.12 1258.4,229 1208.9,221.13 1153.5,205.68 1115.6,194.03", + lp="1298.4,221.5", + pos="e,1104.4,191.41 2673.2,262.67 2298.3,259.24 1389,248.98 1251.4,229 1203.7,222.07 1150.7,206.59 1114.2,194.67", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "chemical to chemical association" -> subject [color=blue, label=subject, - lp="1455.4,221.5", - pos="e,1255.8,191.45 1676.1,255.84 1602.4,250.41 1510.7,241.86 1429.4,229 1373.1,220.1 1309.7,205.16 1265.5,193.93", + lp="1463.4,221.5", + pos="e,1254.8,191.65 2672.1,263.82 2356.8,262.83 1671.7,257.36 1437.4,229 1377.6,221.76 1310.4,206.08 1264.5,194.2", style=solid]; predicate [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1665]; "chemical to chemical association" -> predicate [color=blue, label=predicate, - lp="1573.4,221.5", - pos="e,1416,193.49 1694.3,253.11 1645.8,247.6 1589.6,239.75 1539.4,229 1500.6,220.7 1457.8,207.5 1425.6,196.75", + lp="1601.4,221.5", + pos="e,1418.3,193.17 2671.9,264.1 2379.5,263.51 1775.7,258.6 1567.4,229 1519.5,222.19 1466.4,207.8 1428.2,196.2", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "chemical to chemical association" -> negated [color=blue, label=negated, - lp="1686.4,221.5", - pos="e,1549.5,191.48 1739.1,249.07 1712.9,243.47 1683.7,236.6 1657.4,229 1623.8,219.31 1586.6,205.77 1559.1,195.22", + lp="1745.4,221.5", + pos="e,1553,190.39 2673,262.83 2409,260.26 1896.3,252.34 1716.4,229 1662.6,222.02 1602.4,205.52 1562.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "chemical to chemical association" -> qualifiers [color=blue, label=qualifiers, - lp="1778.9,221.5", - pos="e,1685.9,195.02 1781.5,247.38 1769.9,241.72 1757,235.24 1745.4,229 1728.5,219.92 1710,209.3 1694.6,200.19", + lp="1878.9,221.5", + pos="e,1701.3,193.2 2673,262.73 2434.7,260.11 2000,252.21 1845.4,229 1799.1,222.05 1747.8,207.75 1710.8,196.22", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "chemical to chemical association" -> publications [color=blue, label=publications, - lp="1860.4,221.5", - pos="e,1816.4,196.18 1816.4,246.8 1816.4,235.16 1816.4,219.55 1816.4,206.24", + lp="2016.4,221.5", + pos="e,1851,193.08 2672.9,262.63 2461.4,259.93 2102.3,252.01 1972.4,229 1933.7,222.15 1891.4,208.15 1860.6,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,8 +127,8 @@ digraph { width=2.0943]; "chemical to chemical association" -> "has evidence" [color=blue, label="has evidence", - lp="1977.9,221.5", - pos="e,1954.1,195.69 1867.3,247.74 1881,242.54 1895.6,236.22 1908.4,229 1921.7,221.48 1935.3,211.34 1946.5,202.15", + lp="2162.9,221.5", + pos="e,2006.8,194.09 2674.7,261.51 2496.4,257.79 2219.3,248.95 2116.4,229 2081.9,222.31 2044.4,209.1 2016.3,197.94", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -137,8 +137,8 @@ digraph { width=3.015]; "chemical to chemical association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2141.9,221.5", - pos="e,2134.3,194.73 1917.1,250.88 1952.6,245.34 1992.5,238.04 2028.4,229 2061,220.77 2096.8,208.57 2124.8,198.28", + lp="2301.9,221.5", + pos="e,2190,195.95 2678.7,259.73 2515.6,254.48 2277.6,244.33 2237.4,229 2222.6,223.35 2208.5,212.89 2197.5,202.99", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -147,9 +147,8 @@ digraph { width=3.015]; "chemical to chemical association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2377.4,221.5", - pos="e,2359.2,194.07 1932,252.29 1950.9,250.46 1970.2,248.64 1988.4,247 2087,238.13 2112.7,245.12 2210.4,229 2257.7,221.19 2310.3,207.78 \ -2349.5,196.8", + lp="2468.4,221.5", + pos="e,2385.2,195.77 2673.6,262.33 2548.9,259.31 2393.9,251.09 2373.4,229 2366,220.97 2370.2,211.37 2378,202.74", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -158,9 +157,8 @@ digraph { width=3.015]; "chemical to chemical association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2643.9,221.5", - pos="e,2602.6,194.65 1928.3,251.93 1948.3,250.06 1968.9,248.32 1988.4,247 2204.9,232.32 2262.2,264.24 2476.4,229 2516.3,222.44 2560,209.24 \ -2592.8,198.04", + lp="2677.9,221.5", + pos="e,2595.2,194.17 2677.7,260.19 2630.2,255.5 2586.6,246.37 2571.4,229 2561,217.1 2570.7,206.69 2586.1,198.49", style=solid]; timepoint [color=blue, height=0.5, @@ -169,9 +167,8 @@ digraph { width=1.5346]; "chemical to chemical association" -> timepoint [color=blue, label=timepoint, - lp="2819.4,221.5", - pos="e,2809.4,195.19 1927.3,251.8 1947.6,249.92 1968.6,248.21 1988.4,247 2073.4,241.81 2673.5,255.4 2754.4,229 2771.6,223.39 2788.4,212.2 \ -2801.4,201.82", + lp="2824.4,221.5", + pos="e,2803.6,194.47 2804.8,247.2 2798.6,242.2 2792.9,236.11 2789.4,229 2784.7,219.42 2789.1,209.79 2796.4,201.57", style=solid]; "original subject" [color=blue, height=0.5, @@ -180,9 +177,8 @@ digraph { width=1.0652]; "chemical to chemical association" -> "original subject" [color=blue, label="original subject", - lp="2947.4,221.5", - pos="e,2920.7,194.01 1926.9,251.8 1947.3,249.91 1968.5,248.19 1988.4,247 2084.9,241.24 2765.7,256.61 2858.4,229 2878.1,223.13 2897.7,\ -211.02 2912.5,200.18", + lp="2938.4,221.5", + pos="e,2914.4,192.24 2849,246.75 2858.1,236.6 2870.3,223.86 2882.4,214 2889.6,208.17 2897.8,202.54 2905.7,197.56", style=solid]; "original predicate" [color=blue, height=0.5, @@ -191,47 +187,166 @@ digraph { width=1.5887]; "chemical to chemical association" -> "original predicate" [color=blue, label="original predicate", - lp="3091.9,221.5", - pos="e,3042.5,195.82 1926.9,251.75 1947.3,249.86 1968.5,248.16 1988.4,247 2044.9,243.71 2955.9,252.49 3007.4,229 3019.1,223.68 3029,213.72 \ -3036.5,204.08", + lp="3080.9,221.5", + pos="e,3037.2,195.85 2932.6,250.55 2953.7,245.48 2975.3,238.53 2994.4,229 3007.5,222.46 3020,212.32 3030.1,202.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3184.4,178", + pos="3166.4,178", width=1.0652]; "chemical to chemical association" -> "original object" [color=blue, label="original object", - lp="3224.9,221.5", - pos="e,3180.7,196.04 1926.9,251.71 1947.3,249.83 1968.5,248.14 1988.4,247 2020.9,245.15 3131.9,246.32 3159.4,229 3167.8,223.69 3173.5,\ -214.58 3177.3,205.58", + lp="3208.9,221.5", + pos="e,3163.4,196.13 2949.9,252.29 3036.3,243.32 3140.3,231.98 3144.4,229 3152.1,223.36 3157.1,214.47 3160.4,205.74", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3299.4,178", + width=2.1304]; + "chemical to chemical association" -> "subject category" [color=blue, + label="subject category", + lp="3339.9,221.5", + pos="e,3292.3,196 2949.1,252.2 2968.2,250.37 2987.9,248.56 3006.4,247 3063.7,242.17 3214.4,257.3 3264.4,229 3274.1,223.52 3281.7,214.13 \ +3287.3,204.95", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3470.4,178", + width=2.1304]; + "chemical to chemical association" -> "object category" [color=blue, + label="object category", + lp="3485.9,221.5", + pos="e,3453.9,195.79 2947.2,251.98 2966.9,250.13 2987.2,248.38 3006.4,247 3094.5,240.65 3320.2,258.72 3403.4,229 3419.2,223.36 3434.3,\ +212.65 3446.2,202.59", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3603.4,178", + width=1.0652]; + "chemical to chemical association" -> "subject closure" [color=blue, + label="subject closure", + lp="3621.9,221.5", + pos="e,3587.7,194.71 2946.3,251.88 2966.3,250.01 2986.9,248.29 3006.4,247 3066.2,243.05 3489.6,250.8 3545.4,229 3553.3,225.92 3567.7,\ +213.5 3580.2,201.81", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3699.4,178", + width=1.0652]; + "chemical to chemical association" -> "object closure" [color=blue, + label="object closure", + lp="3741.4,221.5", + pos="e,3697,196.4 2945.8,251.81 2965.9,249.94 2986.8,248.23 3006.4,247 3043.7,244.66 3647.6,250.09 3678.4,229 3686.2,223.67 3691.1,214.85 \ +3694.2,206.08", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3832.4,178", + width=2.1304]; + "chemical to chemical association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3899.9,221.5", + pos="e,3824.8,196.21 2945.3,251.79 2965.6,249.91 2986.6,248.2 3006.4,247 3050.2,244.34 3756.5,249.18 3795.4,229 3805.6,223.73 3813.7,\ +214.24 3819.7,204.93", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4021.4,178", + width=2.1304]; + "chemical to chemical association" -> "object category closure" [color=blue, + label="object category closure", + lp="4089.9,221.5", + pos="e,4016.1,196.12 2944.9,251.76 2965.3,249.87 2986.5,248.16 3006.4,247 3033.7,245.4 3967.7,242.7 3991.4,229 4000.5,223.73 4007.2,214.51 \ +4011.9,205.4", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4211.4,178", + width=1.0652]; + "chemical to chemical association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4261.4,221.5", + pos="e,4204.7,196.2 2944.9,251.71 2965.3,249.83 2986.5,248.14 3006.4,247 3038.9,245.15 4148.8,244.44 4177.4,229 4187.1,223.77 4194.6,\ +214.42 4200,205.21", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4370.4,178", + width=1.0652]; + "chemical to chemical association" -> "object namespace" [color=blue, + label="object namespace", + lp="4414.4,221.5", + pos="e,4363,195.75 2944.4,251.73 2965,249.83 2986.3,248.13 3006.4,247 3043.2,244.94 4300.6,245.82 4333.4,229 4343.7,223.7 4351.9,214.02 \ +4357.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4521.4,178", + width=1.0652]; + "chemical to chemical association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4574.4,221.5", + pos="e,4513.4,195.78 2944.4,251.7 2965,249.81 2986.3,248.11 3006.4,247 3047.3,244.73 4445.7,247.21 4482.4,229 4493.1,223.68 4501.8,213.86 \ +4508.2,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4692.4,178", + width=1.0652]; + "chemical to chemical association" -> "object label closure" [color=blue, + label="object label closure", + lp="4740.9,221.5", + pos="e,4684.1,195.8 2944.4,251.68 2965,249.79 2986.3,248.1 3006.4,247 3052.1,244.5 4611.3,249.03 4652.4,229 4663.3,223.71 4672.1,213.89 \ +4678.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4854.4,178", + width=2.347]; + "chemical to chemical association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4902.9,221.5", + pos="e,4845.8,196.3 2944.4,251.67 2965,249.77 2986.3,248.09 3006.4,247 3056.5,244.28 4769.2,250.98 4814.4,229 4825.1,223.78 4833.9,214.17 \ +4840.4,204.76", style=solid]; type [height=0.5, - pos="3272.4,178", + pos="4988.4,178", width=0.86659]; "chemical to chemical association" -> type [color=blue, label=type, - lp="3302.4,221.5", - pos="e,3281.4,195.57 1926.4,251.73 1947,249.83 1968.3,248.13 1988.4,247 2006.3,245.99 3267.8,241.78 3280.4,229 3286.5,222.79 3286.7,213.89 \ -3284.6,205.31", + lp="5002.4,221.5", + pos="e,4989.2,196.19 2943.9,251.69 2964.7,249.79 2986.2,248.09 3006.4,247 3033.7,245.53 4955,246.04 4976.4,229 4983.2,223.55 4986.6,214.93 \ +4988.2,206.37", style=solid]; category [height=0.5, - pos="3373.4,178", + pos="5089.4,178", width=1.4263]; "chemical to chemical association" -> category [color=blue, label=category, - lp="3375.9,221.5", - pos="e,3361.7,195.89 1926.4,251.72 1947,249.83 1968.3,248.13 1988.4,247 2025.4,244.93 3288.2,243.24 3322.4,229 3335.2,223.66 3346.6,213.42 \ -3355.3,203.58", + lp="5081.9,221.5", + pos="e,5073.8,195.26 2943.9,251.69 2964.7,249.78 2986.2,248.09 3006.4,247 3062.3,243.99 4969.3,246.88 5022.4,229 5038.6,223.54 5054.1,\ +212.52 5066.1,202.21", style=solid]; object [height=0.5, pos="1276.4,91", width=1.0832]; "chemical to chemical association" -> object [color=blue, label=object, - lp="3465.4,178", - pos="e,1315.4,92.482 1926.4,251.71 1947,249.81 1968.3,248.12 1988.4,247 2027.9,244.8 3376.7,247.87 3411.4,229 3439.7,213.63 3455.8,183.12 \ -3433.4,160 3395.5,120.86 1643.8,96.685 1325.7,92.613", + lp="5180.4,178", + pos="e,1315.5,91.926 2943.9,251.68 2964.7,249.78 2986.2,248.08 3006.4,247 3065,243.86 5063.5,252.09 5117.4,229 5148.5,215.69 5173.1,184.11 \ +5149.4,160 5079.1,88.423 1771.3,91.209 1325.8,91.91", style=solid]; subject -> object [label=relation, lp="1275.4,134.5", @@ -244,18 +359,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2035.4,265", + pos="3053.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2166.4,265", + pos="3184.4,265", width=2.0762]; object -> relation [pos="e,1234.2,35.54 1263.9,73.889 1257,64.939 1248.2,53.617 1240.4,43.584", style=dotted]; "chemical to chemical association_object" [color=blue, height=0.5, label="chemical entity", - pos="2341.4,265", + pos="3359.4,265", width=2.2748]; } diff --git a/graphviz/chemical_to_chemical_association.svg b/graphviz/chemical_to_chemical_association.svg index 1a622d687c..21b1998a9b 100644 --- a/graphviz/chemical_to_chemical_association.svg +++ b/graphviz/chemical_to_chemical_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to chemical association - -chemical to chemical association + +chemical to chemical association @@ -24,9 +24,9 @@ chemical to chemical association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ chemical to chemical association->chemical to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ chemical to chemical association->id - - -id + + +id @@ -63,9 +63,9 @@ chemical to chemical association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ chemical to chemical association->name - - -name + + +name @@ -89,9 +89,9 @@ chemical to chemical association->description - - -description + + +description @@ -102,9 +102,9 @@ chemical to chemical association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ chemical to chemical association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ chemical to chemical association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ chemical to chemical association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ chemical to chemical association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ chemical to chemical association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ chemical to chemical association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ chemical to chemical association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ chemical to chemical association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ chemical to chemical association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ chemical to chemical association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ chemical to chemical association->original subject - - -original subject + + +original subject @@ -258,104 +258,247 @@ chemical to chemical association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical to chemical association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical to chemical association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical to chemical association->object category + + +object category + + + +subject closure + +string + + + +chemical to chemical association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical to chemical association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical to chemical association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical to chemical association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical to chemical association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical to chemical association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical to chemical association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical to chemical association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical to chemical association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical to chemical association->type - - -type + + +type - + category - -category + +category - + chemical to chemical association->category - - -category + + +category - + object object - + chemical to chemical association->object - - -object + + +object - + subject->object relation - + relation relation - + subject->relation - + association_type - -string + +string - + association_category - -category type + +category type - + object->relation - + chemical to chemical association_object - -chemical entity + +chemical entity diff --git a/graphviz/chemical_to_chemical_derivation_association.gv b/graphviz/chemical_to_chemical_derivation_association.gv index 3fceaa80da..ba262d2315 100644 --- a/graphviz/chemical_to_chemical_derivation_association.gv +++ b/graphviz/chemical_to_chemical_derivation_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3411.1,283"]; + graph [bb="0,0,5134.1,283"]; node [label="\N"]; "chemical to chemical derivation association" [height=0.5, label="chemical to chemical derivation association", - pos="1838.5,265", + pos="2731.5,265", width=5.9036]; "chemical to chemical association" [height=0.5, pos="162.49,178", width=4.5135]; "chemical to chemical derivation association" -> "chemical to chemical association" [label=is_a, - lp="482.49,221.5", - pos="e,236.63,194.03 1628.4,262.14 1301.7,258.65 686.93,249.54 468.49,229 392.97,221.9 307.88,207.47 246.63,195.93"]; + lp="480.49,221.5", + pos="e,235.5,194.12 2518.6,264.72 2034.1,265.71 860.52,264.25 466.49,229 391.17,222.26 306.32,207.72 245.44,196.04"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "chemical to chemical derivation association" -> id [color=blue, label=id, - lp="600.49,221.5", - pos="e,410.47,190.01 1628.1,262.42 1326.8,259.42 787.38,251.07 593.49,229 519.61,220.59 501.15,215.79 429.49,196 426.38,195.14 423.18,\ -194.18 419.98,193.17", + lp="595.49,221.5", + pos="e,410.47,189.98 2520.4,262.81 2017.5,259.66 776.46,249.85 588.49,229 516.75,221.04 498.99,215.43 429.49,196 426.38,195.13 423.18,\ +194.17 419.98,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical to chemical derivation association" -> iri [color=blue, label=iri, - lp="718.49,221.5", - pos="e,515.1,190.16 1630,261.41 1354.1,257.3 882.49,247.77 710.49,229 631.8,220.41 612.21,215.46 535.49,196 532.06,195.13 528.52,194.16 \ -524.99,193.14", + lp="708.49,221.5", + pos="e,515.4,190.19 2520.8,262.52 2037.6,258.82 877.39,248.06 700.49,229 626.13,220.99 607.87,214.78 535.49,196 532.11,195.12 528.63,\ +194.16 525.15,193.14", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "chemical to chemical derivation association" -> name [color=blue, label=name, - lp="823.49,221.5", - pos="e,640.11,191.18 1628.7,261.96 1373.3,258.59 957.07,250.01 803.49,229 750.08,221.7 690.31,205.92 649.74,194.03", + lp="815.49,221.5", + pos="e,639.24,191.54 2520.2,262.97 2053.4,260.3 962.3,251.68 795.49,229 744.71,222.09 688.12,206.58 649.23,194.65", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "chemical to chemical derivation association" -> description [color=blue, label=description, - lp="942.99,221.5", - pos="e,787.05,193.95 1627.3,263.01 1394.8,260.69 1036.3,253.15 902.49,229 865.98,222.41 826.22,208.97 796.66,197.69", + lp="935.99,221.5", + pos="e,785.29,194.15 2519.2,263.7 2070,262.53 1051.3,256.81 895.49,229 860.65,222.78 822.91,209.42 794.81,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "chemical to chemical derivation association" -> "has attribute" [color=blue, label="has attribute", - lp="1085.5,221.5", - pos="e,927.06,192.73 1629.1,261.8 1430.7,258.45 1147.3,250.05 1038.5,229 1003,222.14 964.46,208.11 936.49,196.66", + lp="1081.5,221.5", + pos="e,926.11,192.95 2519.3,263.49 2096.4,261.91 1176.5,255.44 1034.5,229 1000,222.58 962.73,208.62 935.62,197.07", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical to chemical derivation association" -> negated [color=blue, label=negated, - lp="1234.5,221.5", - pos="e,1047.7,190.33 1629.1,261.93 1505.3,258.34 1345.8,249.61 1205.5,229 1153.9,221.42 1096.1,205.31 1057.6,193.41", + lp="1236.5,221.5", + pos="e,1047.3,190.46 2519,264.63 2161.4,264.76 1454.4,260.78 1207.5,229 1154.9,222.23 1096.2,205.81 1057.3,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical to chemical derivation association" -> qualifiers [color=blue, label=qualifiers, - lp="1365,221.5", - pos="e,1195.8,193.28 1635.6,259.57 1542.4,255.09 1430.8,246.26 1331.5,229 1288.2,221.48 1240.3,207.6 1205.3,196.37", + lp="1375,221.5", + pos="e,1196.2,193.2 2518.7,264.77 2187,264.94 1562,260.8 1341.5,229 1294.8,222.26 1243,207.87 1205.8,196.25", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical to chemical derivation association" -> publications [color=blue, label=publications, - lp="1498.5,221.5", - pos="e,1344.9,193.32 1652.5,256.28 1589.2,251.21 1518.3,242.84 1454.5,229 1420,221.52 1382.4,208.14 1354.4,197.11", + lp="1520.5,221.5", + pos="e,1347.2,192.85 2518.7,264.89 2214.5,265 1670.6,260.53 1476.5,229 1435.1,222.28 1389.6,207.95 1356.9,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "chemical to chemical derivation association" -> "has evidence" [color=blue, label="has evidence", - lp="1638,221.5", - pos="e,1499.4,194.37 1704.3,251.01 1667.4,245.81 1627.6,238.68 1591.5,229 1563.1,221.39 1532.5,209.08 1508.8,198.58", + lp="1679,221.5", + pos="e,1505.5,193.63 2519.4,263.84 2249.1,262.49 1797.1,256.07 1632.5,229 1592.1,222.35 1547.7,208.52 1515.2,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "chemical to chemical derivation association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1767,221.5", - pos="e,1676.9,196.24 1742.7,248.93 1728.4,244.04 1714.5,237.57 1702.5,229 1693.9,222.9 1687,213.84 1681.7,205.1", + lp="1834,221.5", + pos="e,1695,195.61 2523.7,261.12 2262.7,256.78 1840.2,247.06 1769.5,229 1746.4,223.1 1722.4,211.34 1703.7,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "chemical to chemical derivation association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1934.5,221.5", - pos="e,1860.1,194.65 1834.7,246.59 1833.4,236.37 1833.6,223.63 1839.5,214 1842.7,208.82 1846.9,204.35 1851.7,200.52", + lp="2005.5,221.5", + pos="e,1901.5,196.33 2522.3,261.76 2286.4,258.25 1932.7,249.57 1910.5,229 1904.4,223.32 1902,214.91 1901.4,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -130,9 +130,8 @@ digraph { width=3.015]; "chemical to chemical derivation association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2159,221.5", - pos="e,2095.8,194.64 1956.2,250 1980.9,244.97 2006.5,238.18 2029.5,229 2040.8,224.48 2041.7,219.64 2052.5,214 2063.2,208.42 2075,203.13 \ -2086.4,198.44", + lp="2214,221.5", + pos="e,2117.7,195.87 2529.8,259.28 2353.1,254.12 2122.1,244.46 2107.5,229 2100.3,221.43 2103.8,212.05 2110.6,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -141,8 +140,8 @@ digraph { width=1.5346]; "chemical to chemical derivation association" -> timepoint [color=blue, label=timepoint, - lp="2319.5,221.5", - pos="e,2305.5,195.38 1988.6,252.24 2110.3,242.63 2262.2,230.4 2265.5,229 2272.9,225.82 2286.3,214.01 2298.1,202.67", + lp="2368.5,221.5", + pos="e,2320.9,196.43 2540.3,257.11 2446.5,251.95 2350,243.25 2333.5,229 2326.9,223.36 2323.6,214.85 2322,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.0652]; "chemical to chemical derivation association" -> "original subject" [color=blue, label="original subject", - lp="2436.5,221.5", - pos="e,2412.4,193.27 1988.3,252.2 2012.5,250.39 2037.2,248.6 2060.5,247 2126.7,242.47 2295.6,250.13 2358.5,229 2359.8,228.55 2383.5,212.7 \ -2403.9,198.97", + lp="2466.5,221.5", + pos="e,2417.7,194.82 2556.4,254.76 2487.1,249.28 2421.2,241 2410.5,229 2403.8,221.56 2406.4,211.86 2411.9,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.5887]; "chemical to chemical derivation association" -> "original predicate" [color=blue, label="original predicate", - lp="2577,221.5", - pos="e,2532.2,195.46 1985.6,252.01 2010.6,250.18 2036.3,248.43 2060.5,247 2108.6,244.16 2449,247.5 2493.5,229 2500.8,225.96 2513.7,214.16 \ -2525,202.78", + lp="2593,221.5", + pos="e,2533.7,195.8 2585.7,251.87 2559.8,246.73 2538.3,239.42 2529.5,229 2523.6,222.05 2524.9,213.06 2528.8,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -173,102 +170,218 @@ digraph { width=1.0652]; "chemical to chemical derivation association" -> "original object" [color=blue, label="original object", - lp="2707,221.5", - pos="e,2660.1,196.31 1984.4,251.87 2009.8,250.04 2035.9,248.32 2060.5,247 2092.8,245.26 2617.3,248.04 2643.5,229 2650.9,223.62 2655.3,\ -214.91 2657.8,206.25", + lp="2717,221.5", + pos="e,2658.9,196.07 2685.2,247.23 2677.5,242.47 2670.4,236.48 2665.5,229 2661.1,222.32 2659.3,214 2658.9,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2794.5,178", + width=2.1304]; + "chemical to chemical derivation association" -> "subject category" [color=blue, + label="subject category", + lp="2841,221.5", + pos="e,2789.1,196.22 2754.9,247.1 2761.2,241.81 2767.6,235.61 2772.5,229 2777.7,221.97 2782,213.49 2785.4,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2965.5,178", + width=2.1304]; + "chemical to chemical derivation association" -> "object category" [color=blue, + label="object category", + lp="2984,221.5", + pos="e,2949.4,195.91 2843.4,249.66 2864.3,244.69 2885.5,238 2904.5,229 2918.1,222.54 2931.3,212.41 2941.9,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3098.5,178", + width=1.0652]; + "chemical to chemical derivation association" -> "subject closure" [color=blue, + label="subject closure", + lp="3121,221.5", + pos="e,3085.4,195.42 2876.4,251.81 2950.2,244.87 3027.7,236.16 3043.5,229 3056.7,223.04 3068.8,212.72 3078.4,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3198.5,178", + width=1.0652]; + "chemical to chemical derivation association" -> "object closure" [color=blue, + label="object closure", + lp="3241.5,221.5", + pos="e,3196.6,196.18 2883.1,252.39 3012.8,242.42 3178.7,229.57 3179.5,229 3186.9,223.48 3191.4,214.73 3194.1,206.08", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3331.5,178", + width=2.1304]; + "chemical to chemical derivation association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3400,221.5", + pos="e,3324.1,196.07 2880.1,252.13 2904.6,250.31 2929.8,248.53 2953.5,247 2991.5,244.55 3262.1,247.23 3295.5,229 3305.3,223.62 3313.2,\ +214.24 3319,205.05", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3523.5,178", + width=2.1304]; + "chemical to chemical derivation association" -> "object category closure" [color=blue, + label="object category closure", + lp="3591,221.5", + pos="e,3517.5,196.1 2877.7,251.91 2903,250.07 2929,248.35 2953.5,247 2983.3,245.36 3465.5,243.79 3491.5,229 3500.9,223.65 3508,214.27 \ +3513,205.08", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3713.5,178", + width=1.0652]; + "chemical to chemical derivation association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3763.5,221.5", + pos="e,3706.5,196.17 2876.5,251.81 2902.1,249.97 2928.6,248.26 2953.5,247 2993.7,244.96 3643,248.05 3678.5,229 3688.3,223.74 3695.9,214.38 \ +3701.6,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3872.5,178", + width=1.0652]; + "chemical to chemical derivation association" -> "object namespace" [color=blue, + label="object namespace", + lp="3916.5,221.5", + pos="e,3865.1,195.73 2875.9,251.76 2901.7,249.91 2928.4,248.22 2953.5,247 3002.4,244.63 3791.9,251.5 3835.5,229 3845.8,223.66 3854,213.98 \ +3860,204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4023.5,178", + width=1.0652]; + "chemical to chemical derivation association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4076.5,221.5", + pos="e,4015.5,195.76 2875.3,251.74 2901.3,249.88 2928.2,248.19 2953.5,247 3010.7,244.31 3933.2,254.58 3984.5,229 3995.2,223.66 4003.8,\ +213.83 4010.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4194.5,178", + width=1.0652]; + "chemical to chemical derivation association" -> "object label closure" [color=blue, + label="object label closure", + lp="4242,221.5", + pos="e,4186.2,195.78 2875,251.71 2901.1,249.85 2928.1,248.16 2953.5,247 2986.8,245.48 4124.5,243.68 4154.5,229 4165.3,223.68 4174.2,213.86 \ +4180.8,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4338.5,178", + width=2.347]; + "chemical to chemical derivation association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4398,221.5", + pos="e,4335.5,196 2874.7,251.7 2900.9,249.83 2928,248.14 2953.5,247 2991.3,245.3 4283.8,249.62 4315.5,229 4323.6,223.7 4328.9,214.72 \ +4332.4,205.82", style=solid]; type [height=0.5, - pos="2749.5,178", + pos="4472.5,178", width=0.86659]; "chemical to chemical derivation association" -> type [color=blue, label=type, - lp="2783.5,221.5", - pos="e,2760.5,194.96 1983.5,251.83 2009.1,249.98 2035.6,248.27 2060.5,247 2080,246 2748.9,242.97 2762.5,229 2768.9,222.4 2768.1,213.03 \ -2764.8,204.19", + lp="4494.5,221.5", + pos="e,4477.6,196.18 2874.7,251.67 2900.9,249.8 2928,248.13 2953.5,247 2974.5,246.07 4456.5,243.85 4471.5,229 4477.4,223.09 4479,214.51 \ +4478.7,206.12", style=solid]; category [height=0.5, - pos="2850.5,178", + pos="4573.5,178", width=1.4263]; "chemical to chemical derivation association" -> category [color=blue, label=category, - lp="2857,221.5", - pos="e,2840,195.81 1983.5,251.8 2009.1,249.96 2035.6,248.25 2060.5,247 2101.7,244.92 2765.8,245.85 2803.5,229 2815.6,223.61 2826,213.5 \ -2833.9,203.77", + lp="4572,221.5", + pos="e,4559.9,195.45 2874.7,251.66 2900.9,249.79 2928,248.12 2953.5,247 2996.8,245.09 4473.9,244.17 4514.5,229 4529.1,223.56 4542.5,212.8 \ +4552.9,202.65", style=solid]; "catalyst qualifier" [height=0.5, - pos="3008.5,178", + pos="4731.5,178", width=2.4734]; "chemical to chemical derivation association" -> "catalyst qualifier" [color=blue, label="catalyst qualifier", - lp="3000,221.5", - pos="e,2979.5,195.23 1982.9,251.79 2008.7,249.93 2035.4,248.23 2060.5,247 2152.8,242.47 2802.1,248.66 2892.5,229 2919.7,223.08 2948.4,\ -210.75 2970.5,199.81", + lp="4718,221.5", + pos="e,4701.1,194.96 2874.4,251.67 2900.7,249.8 2927.9,248.12 2953.5,247 3045.3,242.99 4517.4,246.99 4607.5,229 4636.9,223.12 4668.3,\ +210.42 4692.1,199.29", style=solid]; subject [height=0.5, - pos="3159.5,178", + pos="4882.5,178", width=1.2277]; "chemical to chemical derivation association" -> subject [color=blue, label=subject, - lp="3129.5,221.5", - pos="e,3138,194.04 1982.6,251.73 2008.5,249.88 2035.3,248.19 2060.5,247 2171.9,241.74 2956.4,256.73 3064.5,229 3087.5,223.08 3111.2,210.62 \ -3129.2,199.62", + lp="4849.5,221.5", + pos="e,4860.2,193.86 2874.4,251.65 2900.7,249.78 2927.9,248.1 2953.5,247 3055,242.62 4683.7,252.83 4782.5,229 4807,223.09 4832.3,210.33 \ +4851.4,199.17", style=solid]; object [height=0.5, - pos="3202.5,91", + pos="4925.5,91", width=1.0832]; "chemical to chemical derivation association" -> object [color=blue, label=object, - lp="3252.5,178", - pos="e,3215.9,108.09 1982.3,251.72 2008.3,249.86 2035.2,248.17 2060.5,247 2121.5,244.17 3100.9,246.26 3159.5,229 3186.1,221.15 3196.2,\ -218.5 3212.5,196 3230.7,170.69 3234.4,156.9 3225.5,127 3224.5,123.55 3223,120.13 3221.2,116.85", + lp="4975.5,178", + pos="e,4938.9,108.09 2874.4,251.64 2900.7,249.77 2927.9,248.1 2953.5,247 3006.9,244.71 4827.9,243.32 4879.5,229 4907.3,221.27 4918.3,\ +219.22 4935.5,196 4954.1,170.92 4957.4,156.9 4948.5,127 4947.5,123.55 4946,120.13 4944.2,116.85", style=solid]; predicate [height=0.5, - pos="3356.5,178", + pos="5079.5,178", width=1.5165]; "chemical to chemical derivation association" -> predicate [color=blue, label=predicate, - lp="3329.5,221.5", - pos="e,3332.6,194.31 1982,251.71 2008.1,249.85 2035.1,248.16 2060.5,247 2126.7,243.97 3189,244.34 3253.5,229 3278.4,223.08 3304.2,210.49 \ -3323.8,199.42", + lp="5052.5,221.5", + pos="e,5055.7,194.36 2874.1,251.65 2900.5,249.77 2927.8,248.1 2953.5,247 3065.8,242.21 4867.1,254.67 4976.5,229 5001.4,223.16 5027.3,\ +210.57 5046.9,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2107.5,265", + pos="3000.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2238.5,265", + pos="3131.5,265", width=2.0762]; "chemical to chemical derivation association_catalyst qualifier" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="2487.5,265", + pos="3380.5,265", width=4.3329]; subject -> object [label=relation, - lp="3197.5,134.5", - pos="e,3184.6,107.23 3160.6,159.55 3161.8,149.57 3164.3,137.07 3169.5,127 3171.7,122.68 3174.6,118.52 3177.8,114.66"]; + lp="4920.5,134.5", + pos="e,4907.6,107.23 4883.6,159.55 4884.8,149.57 4887.3,137.07 4892.5,127 4894.7,122.68 4897.6,118.52 4900.8,114.66"]; relation [height=0.5, - pos="3147.5,18", + pos="4870.5,18", width=1.2999]; - subject -> relation [pos="e,3148.8,36.188 3158.2,159.79 3156.1,132.48 3152,78.994 3149.6,46.38", + subject -> relation [pos="e,4871.8,36.188 4881.2,159.79 4879.1,132.48 4875,78.994 4872.6,46.38", style=dotted]; "chemical to chemical derivation association_subject" [color=blue, height=0.5, label="chemical entity", - pos="2743.5,265", + pos="3636.5,265", width=2.2748]; - object -> relation [pos="e,3160.3,35.54 3190,73.889 3183.1,64.939 3174.3,53.617 3166.5,43.584", + object -> relation [pos="e,4883.3,35.54 4913,73.889 4906.1,64.939 4897.3,53.617 4889.5,43.584", style=dotted]; "chemical to chemical derivation association_object" [color=blue, height=0.5, label="chemical entity", - pos="2925.5,265", + pos="3818.5,265", width=2.2748]; "chemical to chemical derivation association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3103.5,265", + pos="3996.5,265", width=2.1665]; } diff --git a/graphviz/chemical_to_chemical_derivation_association.svg b/graphviz/chemical_to_chemical_derivation_association.svg index 51c44d34d4..80dbbef40c 100644 --- a/graphviz/chemical_to_chemical_derivation_association.svg +++ b/graphviz/chemical_to_chemical_derivation_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to chemical derivation association - -chemical to chemical derivation association + +chemical to chemical derivation association @@ -24,9 +24,9 @@ chemical to chemical derivation association->chemical to chemical association - - -is_a + + +is_a @@ -37,9 +37,9 @@ chemical to chemical derivation association->id - - -id + + +id @@ -50,9 +50,9 @@ chemical to chemical derivation association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical to chemical derivation association->name - - -name + + +name @@ -76,9 +76,9 @@ chemical to chemical derivation association->description - - -description + + +description @@ -89,9 +89,9 @@ chemical to chemical derivation association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ chemical to chemical derivation association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical to chemical derivation association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical to chemical derivation association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ chemical to chemical derivation association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ chemical to chemical derivation association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ chemical to chemical derivation association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ chemical to chemical derivation association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ chemical to chemical derivation association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ chemical to chemical derivation association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ chemical to chemical derivation association->original predicate - - -original predicate + + +original predicate @@ -232,148 +232,291 @@ chemical to chemical derivation association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical to chemical derivation association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical to chemical derivation association->object category + + +object category + + + +subject closure + +string + + + +chemical to chemical derivation association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical to chemical derivation association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical to chemical derivation association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical to chemical derivation association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical to chemical derivation association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical to chemical derivation association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical to chemical derivation association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical to chemical derivation association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical to chemical derivation association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical to chemical derivation association->type - - -type + + +type - + category - -category + +category - + chemical to chemical derivation association->category - - -category + + +category - + catalyst qualifier - -catalyst qualifier + +catalyst qualifier - + chemical to chemical derivation association->catalyst qualifier - - -catalyst qualifier + + +catalyst qualifier - + subject - -subject + +subject - + chemical to chemical derivation association->subject - - -subject + + +subject - + object - -object + +object - + chemical to chemical derivation association->object - - -object + + +object - + predicate - -predicate + +predicate - + chemical to chemical derivation association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + chemical to chemical derivation association_catalyst qualifier - -macromolecular machine mixin + +macromolecular machine mixin - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + chemical to chemical derivation association_subject - -chemical entity + +chemical entity - + object->relation - - + + - + chemical to chemical derivation association_object - -chemical entity + +chemical entity - + chemical to chemical derivation association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv b/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv index 981f1b24c7..ba7c5ffcf3 100644 --- a/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv @@ -1,30 +1,30 @@ digraph { - graph [bb="0,0,4054.4,283"]; + graph [bb="0,0,5769.4,283"]; node [label="\N"]; "chemical to disease or phenotypic feature association" [height=0.5, label="chemical to disease or phenotypic feature association", - pos="2304.4,265", + pos="3355.4,265", width=7.2035]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical to disease or phenotypic feature association" -> association [label=is_a, lp="728.39,221.5", - pos="e,106.71,190.75 2051,261.14 1737.1,256.97 1186.2,247.61 714.39,229 456.4,218.82 389.9,233.14 134.39,196 128.61,195.16 122.61,194.08 \ + pos="e,106.71,190.75 3096.2,264.31 2622.9,264.04 1587.1,259.6 714.39,229 456.36,219.95 389.9,233.14 134.39,196 128.61,195.16 122.61,194.08 \ 116.66,192.88"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical to disease or phenotypic feature association" -> "chemical to entity association mixin" [label=uses, - lp="1035.9,221.5", - pos="e,445.34,190.82 2055.3,259.95 1796.3,255.1 1379.3,245.49 1019.4,229 791.61,218.56 734.74,213.66 507.39,196 490.62,194.7 473,193.23 \ + lp="1034.9,221.5", + pos="e,445.34,190.82 3095.9,264.31 2664.5,263.87 1772.5,258.98 1018.4,229 790.99,219.96 734.29,213.64 507.39,196 490.62,194.7 473,193.23 \ 455.57,191.71"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="790.39,178", width=7.6188]; "chemical to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, - lp="1220.9,221.5", - pos="e,897.79,194.61 2047.9,262.24 1824.7,259.19 1492.8,250.96 1204.4,229 1104,221.35 990.47,207.26 907.73,195.97"]; + lp="1219.9,221.5", + pos="e,894.92,194.71 3097.2,263.17 2608.3,261.05 1563.9,253.69 1203.4,229 1102.1,222.07 987.58,207.68 904.85,196.11"]; id [color=blue, height=0.5, label=string, @@ -32,9 +32,9 @@ digraph { width=1.0652]; "chemical to disease or phenotypic feature association" -> id [color=blue, label=id, - lp="1344.4,221.5", - pos="e,1150.1,189.94 2057.3,259.49 1817.7,254.31 1471.4,244.48 1337.4,229 1261.8,220.26 1242.8,216.09 1169.4,196 1166.2,195.14 1163,194.17 \ -1159.7,193.14", + lp="1340.4,221.5", + pos="e,1150.4,190.01 3099,262.16 2593.9,258.16 1504,247.49 1333.4,229 1259.5,220.99 1241.1,215.79 1169.4,196 1166.3,195.14 1163.1,194.18 \ +1159.9,193.17", style=solid]; iri [color=blue, height=0.5, @@ -43,9 +43,9 @@ digraph { width=1.2277]; "chemical to disease or phenotypic feature association" -> iri [color=blue, label=iri, - lp="1469.4,221.5", - pos="e,1255,190.22 2047.8,262.26 1880.4,258.94 1657.4,250.36 1461.4,229 1377.9,219.9 1356.9,216.2 1275.4,196 1272,195.15 1268.4,194.19 \ -1264.9,193.18", + lp="1460.4,221.5", + pos="e,1255,190.17 3096,264.56 2651.7,264.61 1763,260.59 1452.4,229 1372.8,220.9 1353,215.59 1275.4,196 1272,195.13 1268.4,194.17 1264.9,\ +193.15", style=solid]; name [color=blue, height=0.5, @@ -54,8 +54,8 @@ digraph { width=1.5707]; "chemical to disease or phenotypic feature association" -> name [color=blue, label=name, - lp="1580.4,221.5", - pos="e,1381.7,190.64 2047.8,262.37 1904,258.85 1721.6,250.03 1560.4,229 1501.7,221.35 1435.7,205.21 1391.6,193.33", + lp="1574.4,221.5", + pos="e,1381,191.06 3099.7,261.88 2638.9,257.65 1703.2,246.96 1554.4,229 1497.5,222.13 1433.7,205.99 1390.8,193.89", style=solid]; description [color=blue, height=0.5, @@ -64,8 +64,8 @@ digraph { width=2.0943]; "chemical to disease or phenotypic feature association" -> description [color=blue, label=description, - lp="1708.9,221.5", - pos="e,1531.9,193.22 2074.4,256.65 1924.9,250.85 1744.1,241.62 1668.4,229 1624.8,221.73 1576.6,207.7 1541.5,196.34", + lp="1706.9,221.5", + pos="e,1530.7,193.39 3098.8,262.32 2661,258.91 1803.6,249.67 1666.4,229 1623,222.47 1575.2,208.32 1540.6,196.74", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,8 +74,8 @@ digraph { width=1.4443]; "chemical to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1866.4,221.5", - pos="e,1672.4,191.1 2075.4,256.53 1994.1,251.49 1902.3,243.07 1819.4,229 1771.9,220.94 1719,205.77 1682.3,194.25", + lp="1871.4,221.5", + pos="e,1671.9,191.22 3101.2,261.4 2698.5,256.8 1946.8,246.06 1824.4,229 1774.7,222.06 1719.3,206.31 1681.6,194.33", style=solid]; subject [color=blue, height=0.5, @@ -84,8 +84,8 @@ digraph { width=1.9318]; "chemical to disease or phenotypic feature association" -> subject [color=blue, label=subject, - lp="2013.4,221.5", - pos="e,1822.2,191.56 2148.3,250.61 2096.8,245.17 2039.5,238.01 1987.4,229 1934.2,219.79 1874.3,205.2 1832,194.15", + lp="2030.4,221.5", + pos="e,1821.8,191.63 3097.1,263.15 2765.5,261.03 2208.3,253.78 2004.4,229 1944.6,221.74 1877.4,206.06 1831.6,194.18", style=solid]; predicate [color=blue, height=0.5, @@ -94,8 +94,8 @@ digraph { width=2.1665]; "chemical to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="2127.4,221.5", - pos="e,1981.3,193.75 2192.3,248.73 2160.2,243.45 2125.2,236.86 2093.4,229 2058.6,220.41 2020.3,207.67 1990.9,197.2", + lp="2168.4,221.5", + pos="e,1985.3,193.15 3097,263.44 2794.8,261.57 2313.2,254.51 2134.4,229 2086.5,222.17 2033.4,207.78 1995.2,196.19", style=solid]; negated [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { width=1.2999]; "chemical to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2228.4,221.5", - pos="e,2114.1,192.48 2251.2,247.31 2234.5,241.8 2216.1,235.42 2199.4,229 2173.7,219.12 2145.4,206.72 2123.5,196.74", + lp="2312.4,221.5", + pos="e,2120,190.37 3101.3,261.38 2835.2,257.63 2435.4,248.83 2283.4,229 2229.6,221.98 2169.4,205.49 2129.6,193.35", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=2.1304]; "chemical to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2303.9,221.5", - pos="e,2241.9,195.89 2288.6,246.8 2277.2,234.39 2261.7,217.46 2249,203.62", + lp="2444.9,221.5", + pos="e,2268.1,193.18 3102.1,261.07 2868.5,257.19 2539.4,248.41 2411.4,229 2365.5,222.05 2314.8,207.84 2278,196.34", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=1.7332]; "chemical to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2399.4,221.5", - pos="e,2370.2,195.62 2323.2,246.96 2329.2,241.37 2335.7,235.05 2341.4,229 2349,220.96 2356.9,211.79 2363.8,203.52", + lp="2582.4,221.5", + pos="e,2417.8,193.06 3103.6,260.6 2904.4,256.54 2642.9,247.75 2538.4,229 2500,222.11 2457.9,208.11 2427.3,196.67", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=2.0943]; "chemical to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2525.9,221.5", - pos="e,2514.1,195.08 2386.1,247.85 2406.4,242.79 2428,236.51 2447.4,229 2467.3,221.31 2488.3,210.17 2505.1,200.36", + lp="2727.9,221.5", + pos="e,2573.6,194.18 3112.2,258.66 2953.5,253.77 2761.4,244.81 2681.4,229 2647.4,222.29 2610.6,209.15 2583,198.02", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -144,8 +144,8 @@ digraph { width=3.015]; "chemical to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2696.9,221.5", - pos="e,2697.4,194.5 2448.4,250 2490,244.74 2535.2,237.83 2576.4,229 2614.2,220.9 2655.8,208.25 2687.8,197.7", + lp="2866.9,221.5", + pos="e,2756.6,196.17 3097.7,262.73 2980.5,259.11 2856,250.09 2802.4,229 2788,223.35 2774.5,212.99 2763.9,203.16", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -154,8 +154,8 @@ digraph { width=3.015]; "chemical to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2937.4,221.5", - pos="e,2924,193.85 2482,251.85 2599.7,243.58 2737.4,233.36 2765.4,229 2816,221.13 2872.4,207.5 2914.2,196.45", + lp="3033.4,221.5", + pos="e,2951.1,195.6 3120.2,257.4 3033.2,252.49 2952.1,243.92 2938.4,229 2930.8,220.79 2935.4,211.15 2943.6,202.54", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -164,9 +164,8 @@ digraph { width=3.015]; "chemical to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3206.9,221.5", - pos="e,3167.8,194.61 2484.5,252.01 2514.2,250.21 2544.7,248.47 2573.4,247 2779.1,236.51 2833,261.52 3036.4,229 3078,222.35 3123.7,209.06 \ -3158,197.85", + lp="3242.9,221.5", + pos="e,3160.6,194.03 3188.3,251.21 3164.3,246.1 3144.9,238.96 3136.4,229 3126,216.84 3135.9,206.43 3151.4,198.31", style=solid]; timepoint [color=blue, height=0.5, @@ -175,9 +174,8 @@ digraph { width=1.5346]; "chemical to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3384.4,221.5", - pos="e,3375.2,195.19 2481.6,251.82 2512.2,250 2543.7,248.3 2573.4,247 2656,243.39 3238.5,253.68 3317.4,229 3335.5,223.34 3353.3,211.99 \ -3367.2,201.53", + lp="3391.4,221.5", + pos="e,3371.3,194.53 3352.5,246.62 3351.6,236.66 3351.9,224.16 3356.4,214 3358.3,209.58 3361.2,205.46 3364.4,201.7", style=solid]; "original subject" [color=blue, height=0.5, @@ -186,9 +184,9 @@ digraph { width=1.0652]; "chemical to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3513.4,221.5", - pos="e,3487.2,194.01 2480.9,251.79 2511.7,249.96 2543.5,248.26 2573.4,247 2667.8,243.02 3332.7,255.5 3423.4,229 3443.5,223.13 3463.5,\ -211.02 3478.8,200.18", + lp="3505.4,221.5", + pos="e,3483.3,192.7 3392,247.02 3403.2,241.54 3415.4,235.26 3426.4,229 3437,222.96 3439.1,220.57 3449.4,214 3457.6,208.79 3466.4,203.21 \ +3474.7,198.07", style=solid]; "original predicate" [color=blue, height=0.5, @@ -197,47 +195,165 @@ digraph { width=1.5887]; "chemical to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3657.9,221.5", - pos="e,3609.2,195.83 2480.1,251.75 2511.2,249.91 2543.2,248.22 2573.4,247 2628.9,244.75 3522.7,251.78 3573.4,229 3585.2,223.69 3595.4,\ -213.73 3603.1,204.09", + lp="3644.9,221.5", + pos="e,3602.4,195.43 3498.9,249.98 3520.5,244.94 3541.9,238.15 3561.4,229 3568.9,225.48 3582.7,213.61 3595,202.31", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3751.4,178", + pos="3733.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3790.9,221.5", - pos="e,3747.4,196.06 2479.8,251.71 2510.9,249.87 2543.1,248.19 2573.4,247 2605.4,245.74 3698.2,245.82 3725.4,229 3734,223.71 3739.8,214.61 \ -3743.8,205.6", + lp="3775.9,221.5", + pos="e,3730.4,196.18 3550.7,253.11 3625.8,247.36 3697.2,239.32 3711.4,229 3719.1,223.42 3724.1,214.54 3727.4,205.8", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3866.4,178", + width=2.1304]; + "chemical to disease or phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3906.9,221.5", + pos="e,3859.3,195.98 3539.2,252.28 3670.4,243.63 3824.8,232.74 3831.4,229 3841.1,223.5 3848.7,214.1 3854.3,204.93", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="4037.4,178", + width=2.1304]; + "chemical to disease or phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="4052.9,221.5", + pos="e,4020.9,195.75 3538.1,252.18 3566.9,250.39 3596.5,248.61 3624.4,247 3701.3,242.57 3898,255.15 3970.4,229 3986.1,223.31 4001.3,212.6 \ +4013.2,202.54", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4170.4,178", + width=1.0652]; + "chemical to disease or phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="4188.9,221.5", + pos="e,4154.6,194.71 3535.1,251.98 3564.9,250.18 3595.5,248.44 3624.4,247 3678.6,244.29 4061.9,248.83 4112.4,229 4120.3,225.9 4134.7,\ +213.48 4147.2,201.8", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4266.4,178", + width=1.0652]; + "chemical to disease or phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4308.4,221.5", + pos="e,4264,196.39 3533.3,251.9 3563.7,250.08 3594.9,248.36 3624.4,247 3658.9,245.41 4216.9,248.52 4245.4,229 4253.2,223.66 4258.1,214.83 \ +4261.2,206.07", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4399.4,178", + width=2.1304]; + "chemical to disease or phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4466.9,221.5", + pos="e,4391.8,196.2 3532.6,251.82 3563.2,250 3594.7,248.3 3624.4,247 3665.4,245.21 4326,247.9 4362.4,229 4372.6,223.72 4380.7,214.23 \ +4386.7,204.92", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4588.4,178", + width=2.1304]; + "chemical to disease or phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4656.9,221.5", + pos="e,4583.1,196.12 3531.5,251.76 3562.4,249.93 3594.4,248.24 3624.4,247 3650.3,245.93 4535.9,242 4558.4,229 4567.5,223.73 4574.2,214.5 \ +4578.8,205.39", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4778.4,178", + width=1.0652]; + "chemical to disease or phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4828.4,221.5", + pos="e,4771.7,196.2 3530.8,251.72 3561.9,249.88 3594.1,248.2 3624.4,247 3655.5,245.77 4717,243.78 4744.4,229 4754.1,223.77 4761.6,214.41 \ +4767,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4937.4,178", + width=1.0652]; + "chemical to disease or phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4981.4,221.5", + pos="e,4930,195.75 3530.4,251.69 3561.7,249.85 3594,248.17 3624.4,247 3659.8,245.63 4868.9,245.18 4900.4,229 4910.7,223.7 4918.9,214.02 \ +4924.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="5088.4,178", + width=1.0652]; + "chemical to disease or phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5141.4,221.5", + pos="e,5080.4,195.78 3530.1,251.68 3561.4,249.83 3593.9,248.16 3624.4,247 3664,245.5 5013.9,246.59 5049.4,229 5060.1,223.68 5068.8,213.86 \ +5075.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5259.4,178", + width=1.0652]; + "chemical to disease or phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5307.9,221.5", + pos="e,5251.1,195.8 3529.7,251.66 3561.2,249.81 3593.8,248.14 3624.4,247 3668.7,245.35 5179.6,248.42 5219.4,229 5230.3,223.7 5239.1,213.89 \ +5245.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5421.4,178", + width=2.347]; + "chemical to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5469.9,221.5", + pos="e,5412.8,196.3 3529.7,251.64 3561.2,249.79 3593.8,248.12 3624.4,247 3673.2,245.21 5337.5,250.37 5381.4,229 5392.1,223.78 5400.9,\ +214.17 5407.4,204.76", style=solid]; type [height=0.5, - pos="3839.4,178", + pos="5555.4,178", width=0.86659]; "chemical to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="3868.4,221.5", - pos="e,3847.9,195.59 2479.4,251.69 2510.7,249.85 2543,248.17 2573.4,247 2591.1,246.32 3834,241.59 3846.4,229 3852.5,222.81 3852.8,213.91 \ -3850.9,205.33", + lp="5569.4,221.5", + pos="e,5556.2,196.19 3529.3,251.64 3560.9,249.78 3593.6,248.11 3624.4,247 3651,246.03 5522.5,245.6 5543.4,229 5550.2,223.55 5553.6,214.93 \ +5555.2,206.37", style=solid]; category [height=0.5, - pos="3940.4,178", + pos="5656.4,178", width=1.4263]; "chemical to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="3941.9,221.5", - pos="e,3928.4,195.89 2479.4,251.68 2510.7,249.84 2543,248.17 2573.4,247 2609.9,245.6 3854.6,242.88 3888.4,229 3901.4,223.67 3913,213.43 \ -3921.9,203.59", + lp="5648.9,221.5", + pos="e,5640.8,195.26 3529.3,251.63 3560.9,249.77 3593.6,248.11 3624.4,247 3678.9,245.03 5537.7,246.44 5589.4,229 5605.6,223.54 5621.1,\ +212.51 5633.1,202.2", style=solid]; object [height=0.5, pos="1843.4,91", width=1.0832]; "chemical to disease or phenotypic feature association" -> object [color=blue, label=object, - lp="4032.4,178", - pos="e,1882.4,92.482 2479.1,251.68 2510.4,249.83 2542.9,248.16 2573.4,247 2612.4,245.52 3942.9,247.27 3977.4,229 4006,213.86 4022.9,183.21 \ -4000.4,160 3962.5,120.86 2210.8,96.685 1892.7,92.613", + lp="5747.4,178", + pos="e,1882.5,91.926 3529.3,251.62 3560.9,249.76 3593.6,248.11 3624.4,247 3681.6,244.94 5631.8,251.53 5684.4,229 5715.5,215.69 5740.1,\ +184.11 5716.4,160 5646.1,88.423 2338.3,91.209 1892.8,91.91", style=solid]; subject -> object [label=relation, lp="1842.4,134.5", @@ -250,18 +366,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2620.4,265", + pos="3671.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2751.4,265", + pos="3802.4,265", width=2.0762]; object -> relation [pos="e,1801.2,35.54 1830.9,73.889 1824,64.939 1815.2,53.617 1807.4,43.584", style=dotted]; "chemical to disease or phenotypic feature association_object" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="2993.4,265", + pos="4044.4,265", width=4.1344]; } diff --git a/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg b/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg index 933057c0d4..0fa717a9f3 100644 --- a/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to disease or phenotypic feature association - -chemical to disease or phenotypic feature association + +chemical to disease or phenotypic feature association @@ -24,7 +24,7 @@ chemical to disease or phenotypic feature association->association - + is_a @@ -37,9 +37,9 @@ chemical to disease or phenotypic feature association->chemical to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ chemical to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ chemical to disease or phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ chemical to disease or phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ chemical to disease or phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ chemical to disease or phenotypic feature association->description - - -description + + +description @@ -115,9 +115,9 @@ chemical to disease or phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ chemical to disease or phenotypic feature association->subject - - -subject + + +subject @@ -141,9 +141,9 @@ chemical to disease or phenotypic feature association->predicate - - -predicate + + +predicate @@ -154,9 +154,9 @@ chemical to disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ chemical to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ chemical to disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ chemical to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ chemical to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ chemical to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ chemical to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ chemical to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -258,9 +258,9 @@ chemical to disease or phenotypic feature association->original subject - - -original subject + + +original subject @@ -271,104 +271,247 @@ chemical to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical to disease or phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical to disease or phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical to disease or phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +chemical to disease or phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical to disease or phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical to disease or phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical to disease or phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical to disease or phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical to disease or phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical to disease or phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical to disease or phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical to disease or phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical to disease or phenotypic feature association->type - - -type + + +type - + category - -category + +category - + chemical to disease or phenotypic feature association->category - - -category + + +category - + object object - + chemical to disease or phenotypic feature association->object - - -object + + +object - + subject->object relation - + relation relation - + subject->relation - + association_type - -string + +string - + association_category - -category type + +category type - + object->relation - + chemical to disease or phenotypic feature association_object - -disease or phenotypic feature + +disease or phenotypic feature diff --git a/graphviz/chemical_to_pathway_association.gv b/graphviz/chemical_to_pathway_association.gv index 79b125cdce..0e131e6df9 100644 --- a/graphviz/chemical_to_pathway_association.gv +++ b/graphviz/chemical_to_pathway_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3437.4,283"]; + graph [bb="0,0,5161.4,283"]; node [label="\N"]; "chemical to pathway association" [height=0.5, label="chemical to pathway association", - pos="1814.4,265", + pos="2797.4,265", width=4.4774]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical to pathway association" -> association [label=is_a, - lp="506.39,221.5", - pos="e,107.14,190.59 1654,263.14 1405.1,261.03 910.96,253.81 492.39,229 332.89,219.55 292.09,221.76 134.39,196 128.71,195.07 122.81,193.95 \ -116.94,192.72"]; + lp="496.39,221.5", + pos="e,107.14,190.57 2636.8,263.23 2184,260.81 902.56,252.06 482.39,229 327.27,220.49 287.69,221.24 134.39,196 128.71,195.06 122.81,193.93 \ +116.94,192.71"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical to pathway association" -> "chemical to entity association mixin" [label=uses, - lp="653.89,221.5", - pos="e,398.86,194.21 1655.6,261.77 1381.4,257.51 830.06,246.99 637.39,229 559.73,221.75 472.19,207.47 408.82,196.03"]; + lp="651.89,221.5", + pos="e,397.05,194.27 2636.2,264.34 2203.5,264.79 1023.5,262.77 635.39,229 557.64,222.23 470.01,207.76 406.95,196.12"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "chemical to pathway association" -> id [color=blue, label=id, - lp="776.39,221.5", - pos="e,583.11,189.94 1655.6,261.82 1406.7,257.88 936.04,248.13 769.39,229 694.23,220.37 675.36,216.02 602.39,196 599.24,195.13 595.99,\ -194.16 592.75,193.14", + lp="771.39,221.5", + pos="e,583.38,190 2637.1,262.94 2189.7,259.73 947.96,249.1 764.39,229 691.35,221 673.2,215.65 602.39,196 599.29,195.14 596.09,194.17 \ +592.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "chemical to pathway association" -> iri [color=blue, label=iri, - lp="898.39,221.5", - pos="e,688,190.2 1652.8,264.78 1468,264.08 1156.5,258.02 890.39,229 808.67,220.09 788.15,215.93 708.39,196 704.96,195.14 701.43,194.18 \ -697.89,193.17", + lp="888.39,221.5", + pos="e,688.29,190.23 2636.2,264.61 2238.6,265.54 1218.7,264.28 880.39,229 802.98,220.93 783.81,215.26 708.39,196 705.02,195.14 701.54,\ +194.18 698.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "chemical to pathway association" -> name [color=blue, label=name, - lp="1006.4,221.5", - pos="e,814.2,190.89 1657.4,260.73 1454.2,255.92 1111.5,245.65 986.39,229 930,221.5 866.68,205.55 824.04,193.67", + lp="1000.4,221.5", + pos="e,813.39,191.26 2637.2,262.86 2223.8,259.64 1141.9,249.36 980.39,229 925.75,222.11 864.59,206.19 823.21,194.15", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "chemical to pathway association" -> description [color=blue, label=description, - lp="1130.9,221.5", - pos="e,962.99,193.56 1657.1,260.88 1477.6,256.53 1195.3,247.05 1090.4,229 1049.9,222.04 1005.5,208.3 972.75,196.99", + lp="1128.9,221.5", + pos="e,961.8,193.64 2636.6,263.23 2240.5,260.96 1238.3,252.92 1088.4,229 1048,222.56 1003.8,208.65 971.45,197.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "chemical to pathway association" -> "has attribute" [color=blue, label="has attribute", - lp="1282.4,221.5", - pos="e,1103.2,191.7 1653.2,264.24 1536.3,262 1375.1,253.91 1235.4,229 1193,221.43 1146.1,206.69 1113,195.16", + lp="1286.4,221.5", + pos="e,1103,191.74 2637.4,262.79 2267.5,259.66 1374.5,250.01 1239.4,229 1195.3,222.14 1146.5,206.98 1112.6,195.14", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "chemical to pathway association" -> predicate [color=blue, label=predicate, - lp="1432.4,221.5", - pos="e,1260,193.2 1665.3,258.17 1585.6,253.37 1486.2,244.67 1398.4,229 1354.4,221.14 1305.6,207.36 1269.8,196.25", + lp="1446.4,221.5", + pos="e,1260.6,193.08 2636.1,264.49 2323.2,264.68 1644.1,261.21 1412.4,229 1363.6,222.22 1309.5,207.75 1270.6,196.12", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "chemical to pathway association" -> negated [color=blue, label=negated, - lp="1554.4,221.5", - pos="e,1395.6,189.93 1689.5,253.59 1638.3,248.1 1578.7,240.14 1525.4,229 1475.4,218.56 1464.2,210.87 1415.4,196 1412.1,194.99 1408.7,\ -193.95 1405.2,192.9", + lp="1591.4,221.5", + pos="e,1395,190.21 2636.9,263.29 2351.2,261.39 1765.3,254.41 1562.4,229 1507.1,222.07 1445.1,205.34 1404.5,193.13", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "chemical to pathway association" -> qualifiers [color=blue, label=qualifiers, - lp="1662.9,221.5", - pos="e,1535.3,194.24 1722.8,250.14 1692.8,244.68 1659.4,237.62 1629.4,229 1600.5,220.71 1569.1,208.5 1544.7,198.21", + lp="1726.9,221.5", + pos="e,1543.9,193 2636.9,263.31 2375.8,261.44 1870.4,254.53 1693.4,229 1645.4,222.07 1592,207.62 1553.8,196.03", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "chemical to pathway association" -> publications [color=blue, label=publications, - lp="1766.4,221.5", - pos="e,1676.4,195.45 1763.5,247.74 1749.8,242.54 1735.2,236.22 1722.4,229 1709,221.42 1695.3,211.19 1684.1,201.95", + lp="1867.4,221.5", + pos="e,1694.1,192.76 2636.9,263.25 2401.7,261.29 1975,254.25 1823.4,229 1782.1,222.11 1736.6,207.8 1703.9,196.25", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "chemical to pathway association" -> "has evidence" [color=blue, label="has evidence", - lp="1860.9,221.5", - pos="e,1814.4,196.18 1814.4,246.8 1814.4,235.16 1814.4,219.55 1814.4,206.24", + lp="2018.9,221.5", + pos="e,1851.4,193.77 2638.1,262.23 2435.1,259.11 2095.8,250.74 1972.4,229 1934,222.24 1892.1,208.65 1861,197.35", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "chemical to pathway association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2008.9,221.5", - pos="e,1984.1,195.37 1862.6,247.65 1878.3,242.06 1895.7,235.55 1911.4,229 1932.7,220.11 1955.9,209.19 1975.1,199.83", + lp="2164.9,221.5", + pos="e,2037.8,195.77 2636,264.86 2461.9,264.19 2196.8,258.14 2100.4,229 2081.1,223.17 2061.6,212 2046.3,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "chemical to pathway association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2231.4,221.5", - pos="e,2205,194.37 1929.6,252.4 1975.8,246.78 2029.4,239.04 2077.4,229 2117.3,220.66 2161.4,207.94 2195.3,197.41", + lp="2332.4,221.5", + pos="e,2239.3,196.25 2643.6,259.53 2482.6,254.07 2251.2,243.73 2237.4,229 2231.4,222.6 2232,213.84 2235,205.44", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,9 +147,8 @@ digraph { width=3.015]; "chemical to pathway association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2493.9,221.5", - pos="e,2446.7,194.86 1927,252.05 1946.5,250.2 1966.5,248.43 1985.4,247 2138.5,235.4 2179.4,256.66 2330.4,229 2367,222.3 2406.9,209.38 \ -2437.2,198.36", + lp="2540.9,221.5", + pos="e,2452.3,195.1 2646,258.83 2553,254.04 2449.1,245.14 2434.4,229 2425.6,219.36 2432.6,209.3 2443.9,200.75", style=solid]; timepoint [color=blue, height=0.5, @@ -159,9 +157,8 @@ digraph { width=1.5346]; "chemical to pathway association" -> timepoint [color=blue, label=timepoint, - lp="2667.4,221.5", - pos="e,2653.3,195.38 1925.1,251.85 1945.2,249.98 1965.9,248.25 1985.4,247 2054.1,242.59 2539.7,252.34 2604.4,229 2619.9,223.4 2634.6,\ -212.48 2646,202.26", + lp="2690.4,221.5", + pos="e,2657.3,195.8 2704.6,250.28 2682.1,244.99 2662.4,237.99 2655.4,229 2650.1,222.2 2650.6,213.44 2653.3,205.16", style=solid]; "original subject" [color=blue, height=0.5, @@ -170,9 +167,8 @@ digraph { width=1.0652]; "chemical to pathway association" -> "original subject" [color=blue, label="original subject", - lp="2793.4,221.5", - pos="e,2763.7,194.46 1924.7,251.82 1944.9,249.94 1965.7,248.22 1985.4,247 2065.4,242.03 2630.1,253.41 2706.4,229 2724.5,223.21 2742.2,\ -211.5 2755.8,200.87", + lp="2787.4,221.5", + pos="e,2754.3,191.31 2750.9,247.74 2743.1,242.92 2736.1,236.78 2731.4,229 2724.1,216.95 2733.5,205.59 2745.8,196.74", style=solid]; "original predicate" [color=blue, height=0.5, @@ -181,85 +177,203 @@ digraph { width=1.5887]; "chemical to pathway association" -> "original predicate" [color=blue, label="original predicate", - lp="2934.9,221.5", - pos="e,2885.5,196.26 1924.2,251.8 1944.5,249.91 1965.6,248.19 1985.4,247 2033.5,244.11 2810,250.08 2853.4,229 2864.2,223.74 2873.2,214.12 \ -2879.9,204.71", + lp="2922.9,221.5", + pos="e,2878.4,195.75 2820.8,247.1 2828.2,241.53 2836.3,235.17 2843.4,229 2852.8,220.85 2862.7,211.38 2871.2,202.9", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3026.4,178", + pos="3008.4,178", width=1.0652]; "chemical to pathway association" -> "original object" [color=blue, label="original object", - lp="3066.9,221.5", - pos="e,3023.1,196.01 1924.2,251.75 1944.5,249.86 1965.6,248.16 1985.4,247 2013.6,245.35 2978.6,244.26 3002.4,229 3010.7,223.65 3016.2,\ -214.54 3019.8,205.54", + lp="3052.9,221.5", + pos="e,3006.6,196.32 2914.2,252.53 2947.3,247.2 2977.9,239.61 2990.4,229 2997.2,223.24 3001.4,214.7 3004.1,206.3", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3141.4,178", + width=2.1304]; + "chemical to pathway association" -> "subject category" [color=blue, + label="subject category", + lp="3183.9,221.5", + pos="e,3134.6,196.3 2911.8,252.24 2998.7,243.14 3104.1,231.65 3108.4,229 3117.5,223.43 3124.6,214.32 3129.8,205.38", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3312.4,178", + width=2.1304]; + "chemical to pathway association" -> "object category" [color=blue, + label="object category", + lp="3328.9,221.5", + pos="e,3296.5,195.68 2910.9,252.16 2930.1,250.32 2949.8,248.52 2968.4,247 3030.3,241.93 3189.2,250.89 3247.4,229 3262.8,223.21 3277.5,\ +212.49 3289,202.45", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3445.4,178", + width=1.0652]; + "chemical to pathway association" -> "subject closure" [color=blue, + label="subject closure", + lp="3465.9,221.5", + pos="e,3432.3,195.28 2909.1,251.98 2928.8,250.12 2949.2,248.36 2968.4,247 3015,243.69 3345,246.39 3388.4,229 3402.4,223.38 3415.3,212.75 \ +3425.3,202.73", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3545.4,178", + width=1.0652]; + "chemical to pathway association" -> "object closure" [color=blue, + label="object closure", + lp="3587.4,221.5", + pos="e,3542.9,196.38 2908.1,251.9 2928.2,250.02 2948.9,248.28 2968.4,247 2999.2,244.97 3498.9,246.52 3524.4,229 3532.2,223.65 3537.1,\ +214.82 3540.2,206.06", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3678.4,178", + width=2.1304]; + "chemical to pathway association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3745.9,221.5", + pos="e,3670.7,196.19 2907.7,251.85 2927.9,249.97 2948.7,248.24 2968.4,247 3005.7,244.65 3608.2,246.28 3641.4,229 3651.6,223.71 3659.6,\ +214.21 3665.6,204.91", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3870.4,178", + width=2.1304]; + "chemical to pathway association" -> "object category closure" [color=blue, + label="object category closure", + lp="3936.9,221.5", + pos="e,3864.1,196.16 2907.2,251.8 2927.5,249.91 2948.6,248.19 2968.4,247 3016.6,244.11 3795.1,252.32 3837.4,229 3847,223.73 3854.2,214.37 \ +3859.5,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4060.4,178", + width=1.0652]; + "chemical to pathway association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4109.4,221.5", + pos="e,4053.3,195.73 2907.2,251.74 2927.5,249.85 2948.6,248.15 2968.4,247 2997.7,245.3 3998.4,242.6 4024.4,229 4034.6,223.67 4042.6,213.98 \ +4048.4,204.55", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4219.4,178", + width=1.0652]; + "chemical to pathway association" -> "object namespace" [color=blue, + label="object namespace", + lp="4263.4,221.5", + pos="e,4211.7,195.76 2906.8,251.74 2927.2,249.84 2948.4,248.14 2968.4,247 3002,245.08 4151.3,244.2 4181.4,229 4191.9,223.71 4200.2,214.03 \ +4206.4,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4370.4,178", + width=1.0652]; + "chemical to pathway association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4423.4,221.5", + pos="e,4362.4,195.78 2906.8,251.72 2927.2,249.82 2948.4,248.12 2968.4,247 3006.2,244.88 4297.5,245.84 4331.4,229 4342.1,223.68 4350.8,\ +213.86 4357.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4541.4,178", + width=1.0652]; + "chemical to pathway association" -> "object label closure" [color=blue, + label="object label closure", + lp="4589.9,221.5", + pos="e,4533.1,195.8 2906.8,251.69 2927.2,249.8 2948.4,248.11 2968.4,247 3010.9,244.64 4463.1,247.67 4501.4,229 4512.3,223.7 4521.1,213.88 \ +4527.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4703.4,178", + width=2.347]; + "chemical to pathway association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4751.9,221.5", + pos="e,4694.8,196.3 2906.3,251.72 2926.9,249.81 2948.3,248.1 2968.4,247 3015.4,244.42 4621.1,249.62 4663.4,229 4674.1,223.78 4682.9,214.17 \ +4689.4,204.75", style=solid]; type [height=0.5, - pos="3114.4,178", + pos="4837.4,178", width=0.86659]; "chemical to pathway association" -> type [color=blue, label=type, - lp="3144.4,221.5", - pos="e,3123.4,195.57 1923.8,251.76 1944.2,249.86 1965.4,248.15 1985.4,247 2016.9,245.19 3100.2,251.51 3122.4,229 3128.5,222.79 3128.7,\ -213.88 3126.6,205.3", + lp="4851.4,221.5", + pos="e,4838.2,196.18 2906.3,251.7 2926.9,249.79 2948.3,248.09 2968.4,247 2994.1,245.6 4805.2,245.07 4825.4,229 4832.2,223.54 4835.6,214.93 \ +4837.1,206.37", style=solid]; category [height=0.5, - pos="3215.4,178", + pos="4938.4,178", width=1.4263]; "chemical to pathway association" -> category [color=blue, label=category, - lp="3218.9,221.5", - pos="e,3203.7,195.88 1923.8,251.75 1944.2,249.85 1965.4,248.14 1985.4,247 2050.8,243.26 3103.9,254.23 3164.4,229 3177.2,223.65 3188.6,\ -213.4 3197.3,203.57", + lp="4931.9,221.5", + pos="e,4922.8,195.26 2906.3,251.7 2926.9,249.79 2948.3,248.09 2968.4,247 3021.2,244.13 4821.3,245.89 4871.4,229 4887.6,223.54 4903.1,\ +212.51 4915.1,202.2", style=solid]; subject [height=0.5, - pos="3329.4,178", + pos="5052.4,178", width=1.2277]; "chemical to pathway association" -> subject [color=blue, label=subject, - lp="3312.4,221.5", - pos="e,3312.1,194.76 1923.8,251.73 1944.2,249.84 1965.4,248.13 1985.4,247 2055.8,243.01 3187.1,249.91 3254.4,229 3272.6,223.35 3290.4,\ -211.77 3304.2,201.17", + lp="5028.4,221.5", + pos="e,5033.1,194.33 2906.3,251.69 2926.9,249.78 2948.3,248.09 2968.4,247 3079.3,241 4860.4,258.66 4967.4,229 4988.1,223.25 5009,211.09 \ +5024.9,200.2", style=solid]; object [height=0.5, - pos="3372.4,91", + pos="5095.4,91", width=1.0832]; "chemical to pathway association" -> object [color=blue, label=object, - lp="3415.4,178", - pos="e,3385.8,108.09 1923.8,251.72 1944.2,249.82 1965.4,248.12 1985.4,247 2060.7,242.77 3271.6,254.96 3342.4,229 3384.9,213.41 3390.1,\ -186.96 3395.4,142 3396.2,135.38 3397.3,133.39 3395.4,127 3394.4,123.55 3392.9,120.13 3391.1,116.85", + lp="5139.4,178", + pos="e,5108.8,108.09 2906.3,251.69 2926.9,249.78 2948.3,248.08 2968.4,247 3026.4,243.88 5003.1,246.73 5058.4,229 5082.7,221.2 5091,217.1 \ +5105.4,196 5119.3,175.59 5115.5,166.51 5118.4,142 5119.2,135.38 5120.3,133.39 5118.4,127 5117.4,123.55 5115.9,120.13 5114.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2032.4,265", + pos="3015.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2163.4,265", + pos="3146.4,265", width=2.0762]; subject -> object [label=relation, - lp="3367.4,134.5", - pos="e,3354.5,107.23 3330.5,159.55 3331.7,149.57 3334.2,137.07 3339.4,127 3341.6,122.68 3344.5,118.52 3347.7,114.66"]; + lp="5090.4,134.5", + pos="e,5077.5,107.23 5053.5,159.55 5054.7,149.57 5057.2,137.07 5062.4,127 5064.6,122.68 5067.5,118.52 5070.7,114.66"]; relation [height=0.5, - pos="3317.4,18", + pos="5040.4,18", width=1.2999]; - subject -> relation [pos="e,3318.7,36.188 3328.1,159.79 3326,132.48 3322,78.994 3319.5,46.38", + subject -> relation [pos="e,5041.7,36.188 5051.1,159.79 5049,132.48 5045,78.994 5042.5,46.38", style=dotted]; "chemical to pathway association_subject" [color=blue, height=0.5, label="chemical entity", - pos="2338.4,265", + pos="3321.4,265", width=2.2748]; - object -> relation [pos="e,3330.2,35.54 3359.9,73.889 3353,64.939 3344.2,53.617 3336.4,43.584", + object -> relation [pos="e,5053.2,35.54 5082.9,73.889 5076,64.939 5067.2,53.617 5059.4,43.584", style=dotted]; "chemical to pathway association_object" [color=blue, height=0.5, label=pathway, - pos="2488.4,265", + pos="3471.4,265", width=1.3902]; } diff --git a/graphviz/chemical_to_pathway_association.svg b/graphviz/chemical_to_pathway_association.svg index 62c8a148a8..2ba11e1ebd 100644 --- a/graphviz/chemical_to_pathway_association.svg +++ b/graphviz/chemical_to_pathway_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to pathway association - -chemical to pathway association + +chemical to pathway association @@ -24,9 +24,9 @@ chemical to pathway association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ chemical to pathway association->chemical to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ chemical to pathway association->id - - -id + + +id @@ -63,9 +63,9 @@ chemical to pathway association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ chemical to pathway association->name - - -name + + +name @@ -89,9 +89,9 @@ chemical to pathway association->description - - -description + + +description @@ -102,9 +102,9 @@ chemical to pathway association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ chemical to pathway association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ chemical to pathway association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ chemical to pathway association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ chemical to pathway association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ chemical to pathway association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ chemical to pathway association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ chemical to pathway association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ chemical to pathway association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ chemical to pathway association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ chemical to pathway association->original subject - - -original subject + + +original subject @@ -245,123 +245,266 @@ chemical to pathway association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical to pathway association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +chemical to pathway association->subject category + + +subject category + + + +object category + +ontology class + + + +chemical to pathway association->object category + + +object category + + + +subject closure + +string + + + +chemical to pathway association->subject closure + + +subject closure + + + +object closure + +string + + + +chemical to pathway association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +chemical to pathway association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +chemical to pathway association->object category closure + + +object category closure + + + +subject namespace + +string + + + +chemical to pathway association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +chemical to pathway association->object namespace + + +object namespace + + + +subject label closure + +string + + + +chemical to pathway association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +chemical to pathway association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +chemical to pathway association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + chemical to pathway association->type - - -type + + +type - + category - -category + +category - + chemical to pathway association->category - - -category + + +category - + subject - -subject + +subject - + chemical to pathway association->subject - - -subject + + +subject - + object - -object + +object - + chemical to pathway association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + chemical to pathway association_subject - -chemical entity + +chemical entity - + object->relation - - + + - + chemical to pathway association_object - -pathway + +pathway diff --git a/graphviz/contributor_association.gv b/graphviz/contributor_association.gv index e692740390..57abed7a72 100644 --- a/graphviz/contributor_association.gv +++ b/graphviz/contributor_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,2985.3,283"]; + graph [bb="0,0,4715.3,283"]; node [label="\N"]; "contributor association" [height=0.5, label="contributor association", - pos="1591.4,265", + pos="2444.4,265", width=3.2858]; association [height=0.5, pos="62.394,178", width=1.7332]; "contributor association" -> association [label=is_a, lp="280.39,221.5", - pos="e,103.31,191.77 1473,264.11 1193.3,263.86 497.53,260.01 266.39,229 213.31,221.88 153.98,206.47 113.05,194.62"]; + pos="e,102.91,191.79 2326.4,263.65 1902.4,262.18 470.51,255.32 266.39,229 213.1,222.13 153.57,206.6 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "contributor association" -> id [color=blue, label=id, - lp="397.39,221.5", - pos="e,210.38,189.99 1473.4,263.16 1213.3,260.88 597.47,253.06 390.39,229 317.84,220.57 299.77,215.57 229.39,196 226.29,195.14 223.09,\ + lp="396.39,221.5", + pos="e,210.38,189.98 2326.4,263.27 1918.4,260.59 581.35,250.24 389.39,229 317.23,221.01 299.34,215.5 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "contributor association" -> iri [color=blue, label=iri, - lp="513.39,221.5", - pos="e,315.3,190.22 1473.9,262.58 1232.9,259.28 689.92,249.75 505.39,229 428.91,220.4 409.95,215.12 335.39,196 332.02,195.13 328.54,194.17 \ -325.05,193.16", + lp="504.39,221.5", + pos="e,315.31,190.17 2326.5,263.15 1932.6,260.12 677.42,249.01 496.39,229 423.79,220.98 406.05,214.52 335.39,196 332.02,195.12 328.54,\ +194.14 325.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "contributor association" -> name [color=blue, label=name, - lp="615.39,221.5", - pos="e,439.54,191.46 1473.7,263.06 1247.8,260.74 761.5,253.03 595.39,229 544.84,221.69 488.43,206.31 449.53,194.52", + lp="609.39,221.5", + pos="e,438.3,191.65 2326.4,263.43 1945.1,261.34 760.3,252.98 589.39,229 540.27,222.11 485.63,206.67 447.98,194.75", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "contributor association" -> description [color=blue, label=description, - lp="729.89,221.5", - pos="e,584.31,194.2 1473.2,263.93 1263.8,263.05 835.89,257.66 689.39,229 656.32,222.53 620.59,209.4 593.77,198.22", + lp="725.89,221.5", + pos="e,583.28,194.39 2326,263.95 1957.4,263.47 845.21,259.49 685.39,229 653.14,222.85 618.44,209.7 592.44,198.44", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "contributor association" -> "has attribute" [color=blue, label="has attribute", - lp="866.39,221.5", - pos="e,723.85,193.34 1473.4,263.54 1288.9,261.99 940.46,255.53 819.39,229 789.18,222.38 756.85,208.96 732.92,197.69", + lp="865.39,221.5", + pos="e,723.57,193.54 2326.1,263.95 1976.7,263.46 964.38,259.39 818.39,229 788.46,222.77 756.54,209.42 732.86,198.09", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "contributor association" -> negated [color=blue, label=negated, - lp="1004.4,221.5", - pos="e,845.1,191.3 1476.3,260.79 1325.3,256.01 1068.3,245.72 975.39,229 933.39,221.44 887,206.4 854.66,194.79", + lp="1011.4,221.5", + pos="e,845.52,191.31 2326.7,262.94 2002.8,259.78 1113.3,249.33 982.39,229 937.95,222.1 888.83,206.64 855.05,194.72", style=solid]; publications [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.7332]; "contributor association" -> publications [color=blue, label=publications, - lp="1135.4,221.5", - pos="e,974.82,193.14 1473.1,264 1371.1,262.04 1220.3,254.44 1091.4,229 1054.5,221.72 1014.2,208.05 984.46,196.84", + lp="1154.4,221.5", + pos="e,976.9,192.74 2327,262.66 2023.6,258.96 1228.5,247.59 1110.4,229 1067.5,222.25 1020.3,207.76 986.5,196.1", style=solid]; "has evidence" [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.0943]; "contributor association" -> "has evidence" [color=blue, label="has evidence", - lp="1278.9,221.5", - pos="e,1130,194.11 1477,260.29 1405.9,256.15 1313,247.42 1232.4,229 1200.4,221.69 1165.7,208.84 1139.3,198", + lp="1315.9,221.5", + pos="e,1135.6,193.41 2325.9,264.25 2069.5,264.16 1470.1,260.48 1269.4,229 1226.7,222.3 1179.6,208.24 1145.4,196.73", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=3.015]; "contributor association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1414.9,221.5", - pos="e,1311.5,196.24 1490.4,255.55 1435.9,249.78 1374.9,240.98 1350.4,229 1338.3,223.07 1327.1,213.26 1318.3,203.9", + lp="1474.9,221.5", + pos="e,1326.8,195.38 2326.9,262.56 2074.7,259.11 1497.5,249.11 1410.4,229 1384.4,222.99 1357,210.87 1335.8,200.06", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "contributor association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1581.4,221.5", - pos="e,1502.2,195.39 1514.7,251.18 1503.6,246.04 1493.5,238.9 1486.4,229 1479.5,219.47 1484.9,209.86 1494.2,201.65", + lp="1650.4,221.5", + pos="e,1536.2,196.38 2326.8,262.66 2092.5,259.52 1586.7,250.33 1555.4,229 1547.5,223.65 1542.5,214.82 1539.2,206.06", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "contributor association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1805.9,221.5", - pos="e,1734.7,195.19 1634.5,248.08 1648.1,242.56 1663.1,235.98 1676.4,229 1687.2,223.32 1688.8,220.1 1699.4,214 1707.8,209.16 1716.9,\ -204.28 1725.7,199.76", + lp="1859.9,221.5", + pos="e,1755.7,196.25 2327.4,262.22 2135.4,258.72 1772.8,249.43 1753.4,229 1747.3,222.61 1748,213.84 1751.2,205.44", style=solid]; timepoint [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=1.5346]; "contributor association" -> timepoint [color=blue, label=timepoint, - lp="1964.4,221.5", - pos="e,1942.3,195.93 1675.7,252.33 1690.2,250.45 1705.2,248.6 1719.4,247 1762.2,242.16 1874.7,249.91 1912.4,229 1922.5,223.38 1930.8,\ -213.84 1937,204.58", + lp="2020.4,221.5", + pos="e,1957.5,195.97 2329.9,260.35 2203.7,255.53 2014.6,245.65 1985.4,229 1975.7,223.49 1968.1,214.09 1962.5,204.92", style=solid]; "original subject" [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.0652]; "contributor association" -> "original subject" [color=blue, label="original subject", - lp="2083.4,221.5", - pos="e,2048.7,195.19 1674.3,252.15 1689.3,250.24 1704.8,248.43 1719.4,247 1782.3,240.83 1944.7,252.64 2003.4,229 2017.7,223.24 2031,212.6 \ -2041.4,202.61", + lp="2121.4,221.5", + pos="e,2058.3,196.06 2329.3,260.82 2224.6,256.74 2083.6,247.81 2065.4,229 2059.6,223.03 2057.7,214.54 2057.6,206.25", style=solid]; "original predicate" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.5887]; "contributor association" -> "original predicate" [color=blue, label="original predicate", - lp="2220.9,221.5", - pos="e,2169,196.11 1673.6,251.98 1688.8,250.07 1704.5,248.3 1719.4,247 1766,242.91 2099.2,251.23 2140.4,229 2150.4,223.61 2158.3,214.1 \ -2164.1,204.81", + lp="2254.9,221.5", + pos="e,2177,196.37 2330.3,260.08 2273.5,255.83 2212.5,247.07 2191.4,229 2184.7,223.3 2181,214.77 2178.9,206.37", style=solid]; "original object" [color=blue, height=0.5, @@ -164,102 +160,219 @@ digraph { width=1.0652]; "contributor association" -> "original object" [color=blue, label="original object", - lp="2350.9,221.5", - pos="e,2303.7,196.25 1672.9,251.93 1688.3,250 1704.3,248.24 1719.4,247 1750.9,244.41 2263.1,248.05 2288.4,229 2295.6,223.56 2299.6,214.82 \ -2301.9,206.17", + lp="2385.9,221.5", + pos="e,2310.9,196.03 2375.2,250.34 2360.7,245.28 2346.3,238.39 2334.4,229 2326.5,222.73 2320.2,213.74 2315.4,205.11", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2437.4,178", + width=2.1304]; + "contributor association" -> "subject category" [color=blue, + label="subject category", + lp="2500.9,221.5", + pos="e,2438.8,196.18 2443,246.8 2442,235.16 2440.7,219.55 2439.6,206.24", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2608.4,178", + width=2.1304]; + "contributor association" -> "object category" [color=blue, + label="object category", + lp="2636.9,221.5", + pos="e,2597.2,196.1 2515.2,250.52 2532.1,245.4 2549.6,238.43 2564.4,229 2574.6,222.54 2583.7,213.06 2591,204.09", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2741.4,178", + width=1.0652]; + "contributor association" -> "subject closure" [color=blue, + label="subject closure", + lp="2769.9,221.5", + pos="e,2730.9,195.77 2529.9,252.47 2602.2,242.66 2694.5,230 2696.4,229 2707.6,223.07 2717.3,213.21 2724.9,203.81", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2847.4,178", + width=1.0652]; + "contributor association" -> "object closure" [color=blue, + label="object closure", + lp="2890.4,221.5", + pos="e,2845.6,196.21 2527.6,252.19 2542.5,250.29 2557.9,248.47 2572.4,247 2600.8,244.12 2805.5,246 2828.4,229 2835.8,223.51 2840.3,214.77 \ +2843.1,206.12", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="2980.4,178", + width=2.1304]; + "contributor association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3048.9,221.5", + pos="e,2973,196.09 2526.9,252.01 2542,250.11 2557.7,248.33 2572.4,247 2613.6,243.27 2908,248.75 2944.4,229 2954.4,223.58 2962.3,214.07 \ +2968.1,204.78", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3173.4,178", + width=2.1304]; + "contributor association" -> "object category closure" [color=blue, + label="object category closure", + lp="3239.9,221.5", + pos="e,3167,196.12 2525.9,251.93 2541.3,250 2557.3,248.24 2572.4,247 2603.9,244.42 3112.8,244.4 3140.4,229 3149.9,223.67 3157.2,214.3 \ +3162.4,205.11", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3363.4,178", + width=1.0652]; + "contributor association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3412.4,221.5", + pos="e,3356.3,195.7 2525.5,251.88 2541,249.94 2557.2,248.19 2572.4,247 2614.2,243.73 3290.3,248.57 3327.4,229 3337.6,223.63 3345.6,213.94 \ +3351.4,204.51", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3522.4,178", + width=1.0652]; + "contributor association" -> "object namespace" [color=blue, + label="object namespace", + lp="3565.4,221.5", + pos="e,3514.7,195.74 2525.5,251.83 2541,249.9 2557.2,248.16 2572.4,247 2622.9,243.16 3439.2,251.97 3484.4,229 3494.9,223.68 3503.2,214 \ +3509.4,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3673.4,178", + width=1.0652]; + "contributor association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3725.4,221.5", + pos="e,3665.1,195.78 2525.2,251.84 2540.8,249.89 2557.1,248.14 2572.4,247 2631.2,242.61 3580.5,254.99 3633.4,229 3644.2,223.67 3653.1,\ +213.85 3659.7,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3844.4,178", + width=1.0652]; + "contributor association" -> "object label closure" [color=blue, + label="object label closure", + lp="3890.9,221.5", + pos="e,3835.8,195.8 2525.2,251.81 2540.8,249.87 2557.1,248.13 2572.4,247 2606.5,244.49 3772.6,243.85 3803.4,229 3814.4,223.7 3823.4,213.88 \ +3830.2,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="3988.4,178", + width=2.347]; + "contributor association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4046.9,221.5", + pos="e,3985.1,196.03 2525.2,251.79 2540.8,249.85 2557.1,248.11 2572.4,247 2611,244.2 3931.8,249.81 3964.4,229 3972.7,223.67 3978.3,214.56 \ +3981.9,205.56", style=solid]; type [height=0.5, - pos="2392.4,178", + pos="4122.4,178", width=0.86659]; "contributor association" -> type [color=blue, label=type, - lp="2427.4,221.5", - pos="e,2403.8,194.93 1672.9,251.87 1688.3,249.94 1704.3,248.2 1719.4,247 1738.4,245.49 2393.1,242.67 2406.4,229 2412.9,222.36 2411.9,\ -212.99 2408.4,204.15", + lp="4143.4,221.5", + pos="e,4127.1,196.23 2525.2,251.77 2540.8,249.83 2557.1,248.1 2572.4,247 2593.8,245.46 4105,243.99 4120.4,229 4126.4,223.15 4128.2,214.58 \ +4128,206.19", style=solid]; category [height=0.5, - pos="2493.4,178", + pos="4223.4,178", width=1.4263]; "contributor association" -> category [color=blue, label=category, - lp="2499.9,221.5", - pos="e,2483.2,195.8 1672.5,251.89 1688,249.95 1704.2,248.19 1719.4,247 1759.7,243.83 2410.6,245.71 2447.4,229 2459.2,223.65 2469.3,213.69 \ -2477.1,204.05", + lp="4220.9,221.5", + pos="e,4209.5,195.46 2525.2,251.77 2540.8,249.83 2557.1,248.1 2572.4,247 2616.5,243.83 4121.9,244.28 4163.4,229 4178.1,223.57 4191.8,\ +212.81 4202.4,202.66", style=solid]; subject [height=0.5, - pos="2607.4,178", + pos="4337.4,178", width=1.2277]; "contributor association" -> subject [color=blue, label=subject, - lp="2591.4,221.5", - pos="e,2590.9,194.71 1672.5,251.86 1688,249.92 1704.2,248.17 1719.4,247 1809.8,240.02 2449.2,257.06 2535.4,229 2552.8,223.32 2569.8,211.9 \ -2582.9,201.4", + lp="4316.4,221.5", + pos="e,4318.9,194.56 2525.2,251.76 2540.8,249.82 2557.1,248.09 2572.4,247 2665.7,240.33 4166.5,255.02 4256.4,229 4276,223.31 4295.6,211.45 \ +4310.6,200.7", style=solid]; predicate [height=0.5, - pos="2724.4,178", + pos="4454.4,178", width=1.5165]; "contributor association" -> predicate [color=blue, label=predicate, - lp="2697.4,221.5", - pos="e,2700.5,194.27 1672.5,251.83 1688,249.9 1704.2,248.16 1719.4,247 1819.3,239.39 2523.9,252.43 2621.4,229 2646.3,223.02 2672.1,210.43 \ -2691.7,199.38", + lp="4424.4,221.5", + pos="e,4429.7,194.11 2524.8,251.8 2540.6,249.84 2557,248.1 2572.4,247 2670.7,240 4250.2,250.69 4346.4,229 4372.6,223.09 4400.1,210.27 \ +4420.7,199.1", style=solid]; object [height=0.5, - pos="2674.4,91", + pos="4404.4,91", width=1.0832]; "contributor association" -> object [color=blue, label=object, - lp="2816.4,178", - pos="e,2706.5,101.28 1672.2,251.85 1687.8,249.9 1704.1,248.15 1719.4,247 1832,238.55 2627.1,260.99 2735.4,229 2772.5,218.04 2807.5,193.63 \ -2788.4,160 2773,132.81 2741.9,115.34 2716,104.93", + lp="4546.4,178", + pos="e,4434.2,102.71 2524.8,251.79 2540.6,249.83 2557,248.09 2572.4,247 2677.1,239.57 4361.2,257.11 4462.4,229 4490.2,221.27 4504.1,221.08 \ +4518.4,196 4540.7,156.94 4484.7,124.38 4443.5,106.59", style=solid]; qualifiers [height=0.5, - pos="2931.4,178", + pos="4661.4,178", width=1.4985]; "contributor association" -> qualifiers [color=blue, label=qualifiers, - lp="2902.9,221.5", - pos="e,2907.8,194.3 1672.2,251.83 1687.8,249.88 1704.1,248.14 1719.4,247 1842.4,237.86 2709.5,257.84 2829.4,229 2854.1,223.07 2879.7,\ -210.47 2899.1,199.41", + lp="4632.9,221.5", + pos="e,4637.8,194.36 2524.8,251.78 2540.6,249.83 2557,248.09 2572.4,247 2682.5,239.22 4452,254.43 4559.4,229 4584.1,223.16 4609.7,210.56 \ +4629.1,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1766.4,265", + pos="2619.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1897.4,265", + pos="2750.4,265", width=2.0762]; subject -> object [label=relation, - lp="2673.4,134.5", - pos="e,2661.7,108.05 2620.3,160.61 2630.3,147.95 2644.3,130.24 2655.5,115.98"]; + lp="4403.4,134.5", + pos="e,4391.7,108.05 4350.3,160.61 4360.3,147.95 4374.3,130.24 4385.5,115.98"]; relation [height=0.5, - pos="2619.4,18", + pos="4349.4,18", width=1.2999]; - subject -> relation [pos="e,2618.1,36.188 2608.7,159.79 2610.8,132.48 2614.8,78.994 2617.3,46.38", + subject -> relation [pos="e,4348.1,36.188 4338.7,159.79 4340.8,132.48 4344.8,78.994 4347.3,46.38", style=dotted]; "contributor association_subject" [color=blue, height=0.5, label="information content entity", - pos="2123.4,265", + pos="2976.4,265", width=3.7011]; "contributor association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2352.4,265", + pos="3205.4,265", width=2.1665]; - object -> relation [pos="e,2632.2,35.54 2661.9,73.889 2655,64.939 2646.2,53.617 2638.4,43.584", + object -> relation [pos="e,4362.2,35.54 4391.9,73.889 4385,64.939 4376.2,53.617 4368.4,43.584", style=dotted]; "contributor association_object" [color=blue, height=0.5, label=agent, - pos="2485.4,265", + pos="3338.4,265", width=1.0291]; "contributor association_qualifiers" [color=blue, height=0.5, label="ontology class", - pos="2617.4,265", + pos="3470.4,265", width=2.1304]; } diff --git a/graphviz/contributor_association.svg b/graphviz/contributor_association.svg index d5ae7e38be..be5993866b 100644 --- a/graphviz/contributor_association.svg +++ b/graphviz/contributor_association.svg @@ -4,16 +4,16 @@ - + %3 - + contributor association - -contributor association + +contributor association @@ -24,8 +24,8 @@ contributor association->association - - + + is_a @@ -37,9 +37,9 @@ contributor association->id - - -id + + +id @@ -50,9 +50,9 @@ contributor association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ contributor association->name - - -name + + +name @@ -76,9 +76,9 @@ contributor association->description - - -description + + +description @@ -89,9 +89,9 @@ contributor association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ contributor association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ contributor association->publications - - -publications + + +publications @@ -128,9 +128,9 @@ contributor association->has evidence - - -has evidence + + +has evidence @@ -141,9 +141,9 @@ contributor association->knowledge source - - -knowledge source + + +knowledge source @@ -154,9 +154,9 @@ contributor association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -167,9 +167,9 @@ contributor association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -180,9 +180,9 @@ contributor association->timepoint - - -timepoint + + +timepoint @@ -193,9 +193,9 @@ contributor association->original subject - - -original subject + + +original subject @@ -206,9 +206,9 @@ contributor association->original predicate - - -original predicate + + +original predicate @@ -219,148 +219,291 @@ contributor association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +contributor association->subject category + + +subject category + + + +object category + +ontology class + + + +contributor association->object category + + +object category + + + +subject closure + +string + + + +contributor association->subject closure + + +subject closure + + + +object closure + +string + + + +contributor association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +contributor association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +contributor association->object category closure + + +object category closure + + + +subject namespace + +string + + + +contributor association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +contributor association->object namespace + + +object namespace + + + +subject label closure + +string + + + +contributor association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +contributor association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +contributor association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + contributor association->type - - -type + + +type - + category - -category + +category - + contributor association->category - - -category + + +category - + subject - -subject + +subject - + contributor association->subject - - -subject + + +subject - + predicate - -predicate + +predicate - + contributor association->predicate - - -predicate + + +predicate - + object - -object + +object - + contributor association->object - - -object + + +object - + qualifiers - -qualifiers + +qualifiers - + contributor association->qualifiers - - -qualifiers + + +qualifiers - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + contributor association_subject - -information content entity + +information content entity - + contributor association_predicate - -predicate type + +predicate type - + object->relation - - + + - + contributor association_object - -agent + +agent - + contributor association_qualifiers - -ontology class + +ontology class diff --git a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv index 1b492005e9..dff5eb113d 100644 --- a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv +++ b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3614.4,283"]; + graph [bb="0,0,5342.4,283"]; node [label="\N"]; "disease or phenotypic feature to genetic inheritance association" [height=0.5, label="disease or phenotypic feature to genetic inheritance association", - pos="1991.4,265", + pos="2970.4,265", width=8.5576]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease or phenotypic feature to genetic inheritance association" -> association [label=is_a, - lp="665.39,221.5", - pos="e,106.72,190.7 1697.9,259.51 1426.3,254.6 1011.5,245.19 651.39,229 421.38,218.66 362.13,229.91 134.39,196 128.62,195.14 122.62,194.05 \ -116.66,192.84"]; + lp="664.39,221.5", + pos="e,106.72,190.7 2662.5,264.13 2218.1,263.23 1370.9,257.46 650.39,229 420.77,219.93 361.69,229.86 134.39,196 128.62,195.14 122.62,\ +194.05 116.66,192.83"]; "disease or phenotypic feature to entity association mixin" [height=0.5, pos="417.39,178", width=7.6188]; "disease or phenotypic feature to genetic inheritance association" -> "disease or phenotypic feature to entity association mixin" [label=uses, - lp="847.89,221.5", - pos="e,524.36,194.6 1686.6,262.29 1452.4,259.16 1121.1,250.82 831.39,229 730.8,221.42 617.07,207.28 534.3,195.97"]; + lp="845.89,221.5", + pos="e,521.67,194.71 2664.2,262.94 2160,260.52 1176.4,252.83 829.39,229 728.37,222.06 614.1,207.67 531.57,196.11"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> id [color=blue, label=id, - lp="969.39,221.5", - pos="e,777.12,189.93 1698.8,259.33 1445.7,254.32 1099.5,244.85 962.39,229 887.67,220.36 868.92,215.94 796.39,196 793.24,195.13 790,194.16 \ -786.75,193.13", + lp="965.39,221.5", + pos="e,777.38,190 2667.2,261.79 2146.7,257.55 1122.9,247.04 958.39,229 885.35,220.99 867.2,215.65 796.39,196 793.29,195.14 790.09,194.17 \ +786.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "disease or phenotypic feature to genetic inheritance association" -> iri [color=blue, label=iri, - lp="1091.4,221.5", - pos="e,882,190.19 1685.1,262.99 1508.7,259.71 1283,250.94 1083.4,229 1002.1,220.07 981.72,215.86 902.39,196 898.96,195.14 895.43,194.18 \ -891.89,193.16", + lp="1081.4,221.5", + pos="e,882.3,190.23 2662.2,264.76 2205.7,264.78 1371.7,260.3 1073.4,229 996.41,220.92 977.38,215.19 902.39,196 899.02,195.14 895.54,194.18 \ +892.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "disease or phenotypic feature to genetic inheritance association" -> name [color=blue, label=name, - lp="1199.4,221.5", - pos="e,1008,190.88 1712.6,257.34 1519.1,251.7 1279,242.37 1179.4,229 1123.3,221.47 1060.2,205.52 1017.8,193.65", + lp="1192.4,221.5", + pos="e,1007,191.24 2667.7,261.66 2193.8,257.46 1315.9,247.33 1172.4,229 1118.3,222.08 1057.7,206.16 1016.7,194.13", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "disease or phenotypic feature to genetic inheritance association" -> description [color=blue, label=description, - lp="1322.9,221.5", - pos="e,1156.5,193.56 1713.1,257.26 1551,251.96 1363.1,243.06 1282.4,229 1242.4,222.03 1198.5,208.29 1166.2,196.98", + lp="1319.9,221.5", + pos="e,1155.4,193.76 2665.4,262.31 2215.3,259.12 1411.7,250.47 1279.4,229 1239.9,222.58 1196.6,208.74 1164.9,197.24", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "disease or phenotypic feature to genetic inheritance association" -> "has attribute" [color=blue, label="has attribute", - lp="1473.4,221.5", - pos="e,1296.8,191.81 1700.2,259.09 1611.7,254.08 1514.6,245.03 1426.4,229 1384.8,221.45 1338.9,206.77 1306.5,195.27", + lp="1475.4,221.5", + pos="e,1296.6,191.98 2667.9,261.54 2253.5,257.49 1546.7,247.91 1428.4,229 1385.9,222.22 1339.2,207.3 1306.3,195.52", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "disease or phenotypic feature to genetic inheritance association" -> subject [color=blue, label=subject, - lp="1617.4,221.5", - pos="e,1445.5,192.43 1776.7,252.08 1716.5,246.87 1651.1,239.48 1591.4,229 1544.7,220.81 1492.6,206.55 1455.2,195.36", + lp="1630.4,221.5", + pos="e,1445.6,192.36 2662.6,263.9 2323.7,262.41 1801,255.64 1604.4,229 1552.9,222.02 1495.4,206.97 1455.2,195.2", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "disease or phenotypic feature to genetic inheritance association" -> negated [color=blue, label=negated, - lp="1731.4,221.5", - pos="e,1572.6,189.93 1831.6,249.59 1789.4,244.44 1744,237.68 1702.4,229 1652.4,218.56 1641.2,210.87 1592.4,196 1589.1,194.99 1585.7,193.95 \ -1582.2,192.9", + lp="1767.4,221.5", + pos="e,1572.1,190.32 2666.1,262.1 2360.5,258.97 1910.8,250.73 1738.4,229 1683.6,222.1 1622.3,205.5 1581.9,193.31", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "disease or phenotypic feature to genetic inheritance association" -> qualifiers [color=blue, label=qualifiers, - lp="1839.9,221.5", - pos="e,1712.3,194.24 1888.3,248.01 1861.4,242.88 1832.6,236.53 1806.4,229 1777.5,220.71 1746.1,208.5 1721.7,198.21", + lp="1901.9,221.5", + pos="e,1720.8,193.12 2666.6,262.01 2394.5,258.83 2016.4,250.55 1868.4,229 1821,222.1 1768.4,207.72 1730.6,196.15", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "disease or phenotypic feature to genetic inheritance association" -> publications [color=blue, label=publications, - lp="1943.4,221.5", - pos="e,1853.4,195.45 1939.1,247.2 1925.8,242.09 1911.7,235.97 1899.4,229 1886,221.42 1872.3,211.19 1861.1,201.95", + lp="2042.4,221.5", + pos="e,1871,192.88 2667.3,261.71 2430.9,258.3 2122.3,249.87 1998.4,229 1957.7,222.14 1912.9,207.9 1880.6,196.36", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "disease or phenotypic feature to genetic inheritance association" -> "has evidence" [color=blue, label="has evidence", - lp="2037.9,221.5", - pos="e,1991.4,196.18 1991.4,246.8 1991.4,235.16 1991.4,219.55 1991.4,206.24", + lp="2192.9,221.5", + pos="e,2027.9,193.89 2675.4,259.8 2481,255.44 2244.8,246.63 2146.4,229 2108.8,222.27 2067.8,208.75 2037.4,197.47", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "disease or phenotypic feature to genetic inheritance association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2185.9,221.5", - pos="e,2161.1,195.37 2041.1,247.12 2056.4,241.65 2073.2,235.34 2088.4,229 2109.7,220.11 2132.9,209.19 2152.1,199.83", + lp="2337.9,221.5", + pos="e,2213.7,195.77 2696.2,256.8 2518.9,251 2313.9,241.72 2273.4,229 2254.8,223.17 2236.3,212 2221.7,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "disease or phenotypic feature to genetic inheritance association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2408.4,221.5", - pos="e,2382,194.37 2133.3,249.01 2172.7,243.79 2215.4,237.15 2254.4,229 2294.3,220.66 2338.4,207.94 2372.3,197.41", + lp="2505.4,221.5", + pos="e,2414.3,196.1 2708.9,255.46 2568.3,249.55 2421.3,240.65 2410.4,229 2404.2,222.38 2405.4,213.47 2409.3,204.99", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,8 +147,8 @@ digraph { width=3.015]; "disease or phenotypic feature to genetic inheritance association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2670.9,221.5", - pos="e,2623.4,194.8 2204.4,251.98 2332.9,244.31 2477.3,234.75 2507.4,229 2543.8,222.03 2583.6,209.19 2613.9,198.27", + lp="2714.9,221.5", + pos="e,2627.2,195.05 2735.9,253.3 2672.6,248.03 2618.6,240.28 2608.4,229 2599.4,219.14 2606.6,209.11 2618.4,200.64", style=solid]; timepoint [color=blue, height=0.5, @@ -158,9 +157,8 @@ digraph { width=1.5346]; "disease or phenotypic feature to genetic inheritance association" -> timepoint [color=blue, label=timepoint, - lp="2839.4,221.5", - pos="e,2827.3,195.23 2205.8,252.05 2240.1,250.27 2275.2,248.52 2308.4,247 2360.9,244.59 2732,247.06 2781.4,229 2789.8,225.92 2805.6,213.58 \ -2819.4,201.93", + lp="2863.4,221.5", + pos="e,2832.3,195.65 2868.4,247.98 2849.9,243.01 2834.5,236.74 2828.4,229 2822.9,221.97 2824,213.06 2827.6,204.71", style=solid]; "original subject" [color=blue, height=0.5, @@ -169,9 +167,8 @@ digraph { width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "original subject" [color=blue, label="original subject", - lp="2957.4,221.5", - pos="e,2935.3,192.7 2204.1,251.95 2238.9,250.16 2274.7,248.44 2308.4,247 2371.7,244.3 2817.9,248.01 2878.4,229 2890,225.34 2891.1,220.57 \ -2901.4,214 2909.6,208.79 2918.4,203.21 2926.7,198.07", + lp="2960.4,221.5", + pos="e,2929.7,190.76 2922.9,247.11 2915.5,242.39 2908.9,236.45 2904.4,229 2896.7,216.25 2907.3,204.67 2920.9,195.86", style=solid]; "original predicate" [color=blue, height=0.5, @@ -180,9 +177,8 @@ digraph { width=1.5887]; "disease or phenotypic feature to genetic inheritance association" -> "original predicate" [color=blue, label="original predicate", - lp="3098.9,221.5", - pos="e,3054.9,195.51 2202.4,251.86 2237.8,250.06 2274.1,248.36 2308.4,247 2347.5,245.45 2976.8,243.11 3013.4,229 3021.1,226.01 3035.2,\ -214.01 3047.5,202.51", + lp="3097.9,221.5", + pos="e,3053.9,195.61 2993.6,246.94 3001,241.36 3009.1,235.03 3016.4,229 3026.5,220.62 3037.2,211.01 3046.5,202.48", style=solid]; "original object" [color=blue, height=0.5, @@ -191,45 +187,162 @@ digraph { width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "original object" [color=blue, label="original object", - lp="3227.9,221.5", - pos="e,3182.6,196.44 2201.1,251.79 2236.9,249.98 2273.7,248.3 2308.4,247 2332.1,246.11 3143.6,242.19 3163.4,229 3171.3,223.72 3176.4,\ -214.91 3179.7,206.14", + lp="3228.9,221.5", + pos="e,3182.8,196.36 3108,248.87 3133.4,243.87 3155.1,237.37 3165.4,229 3172.5,223.23 3177.1,214.57 3180,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3318.4,178", + width=2.1304]; + "disease or phenotypic feature to genetic inheritance association" -> "subject category" [color=blue, + label="subject category", + lp="3359.9,221.5", + pos="e,3311.3,196.31 3190.9,252.43 3231.4,247.26 3266.5,239.79 3284.4,229 3293.7,223.39 3301,214.15 3306.5,205.12", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3489.4,178", + width=2.1304]; + "disease or phenotypic feature to genetic inheritance association" -> "object category" [color=blue, + label="object category", + lp="3504.9,221.5", + pos="e,3473.1,195.61 3191.5,252.46 3295,246.04 3400.7,237.62 3423.4,229 3438.9,223.12 3453.8,212.38 3465.6,202.36", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3622.4,178", + width=1.0652]; + "disease or phenotypic feature to genetic inheritance association" -> "subject closure" [color=blue, + label="subject closure", + lp="3642.9,221.5", + pos="e,3609,195.21 3185.5,252.11 3353.7,242.7 3559.9,230.83 3564.4,229 3578.5,223.27 3591.6,212.63 3601.8,202.63", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3720.4,178", + width=1.0652]; + "disease or phenotypic feature to genetic inheritance association" -> "object closure" [color=blue, + label="object closure", + lp="3762.4,221.5", + pos="e,3718.3,196.32 3186.1,252.14 3220,250.36 3254.6,248.59 3287.4,247 3310.3,245.89 3681.7,242.29 3700.4,229 3708,223.64 3712.7,214.92 \ +3715.6,206.26", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3853.4,178", + width=2.1304]; + "disease or phenotypic feature to genetic inheritance association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3920.9,221.5", + pos="e,3845.7,196.16 3183.5,252 3218.2,250.21 3253.8,248.47 3287.4,247 3316.8,245.71 3790.4,242.68 3816.4,229 3826.5,223.67 3834.6,214.17 \ +3840.6,204.87", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4043.4,178", + width=2.1304]; + "disease or phenotypic feature to genetic inheritance association" -> "object category closure" [color=blue, + label="object category closure", + lp="4110.9,221.5", + pos="e,4037.7,196.12 3180.9,251.86 3216.5,250.05 3253,248.35 3287.4,247 3327.7,245.42 3977.4,249.03 4012.4,229 4021.6,223.72 4028.4,214.49 \ +4033.3,205.39", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4233.4,178", + width=1.0652]; + "disease or phenotypic feature to genetic inheritance association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4283.4,221.5", + pos="e,4226.4,196.2 3179.7,251.77 3215.6,249.96 3252.6,248.28 3287.4,247 3338,245.14 4153.7,252.82 4198.4,229 4208.2,223.76 4215.9,214.41 \ +4221.5,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4392.4,178", + width=1.0652]; + "disease or phenotypic feature to genetic inheritance association" -> "object namespace" [color=blue, + label="object namespace", + lp="4436.4,221.5", + pos="e,4385,195.74 3178.8,251.73 3215,249.91 3252.3,248.24 3287.4,247 3317,245.96 4329,242.58 4355.4,229 4365.7,223.68 4373.9,214 4379.9,\ +204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4543.4,178", + width=1.0652]; + "disease or phenotypic feature to genetic inheritance association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4596.4,221.5", + pos="e,4535.4,195.77 3178.4,251.69 3214.7,249.87 3252.1,248.21 3287.4,247 3321.2,245.84 4474.1,244.06 4504.4,229 4515.1,223.67 4523.8,\ +213.85 4530.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4714.4,178", + width=1.0652]; + "disease or phenotypic feature to genetic inheritance association" -> "object label closure" [color=blue, + label="object label closure", + lp="4761.9,221.5", + pos="e,4706.1,195.79 3177.9,251.66 3214.4,249.84 3252,248.18 3287.4,247 3325.9,245.72 4639.8,245.92 4674.4,229 4685.3,223.69 4694.1,213.88 \ +4700.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4867.4,178", + width=2.347]; + "disease or phenotypic feature to genetic inheritance association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4920.9,221.5", + pos="e,4861.4,196.18 3177.5,251.64 3214.1,249.81 3251.9,248.16 3287.4,247 3330.4,245.6 4797.8,249.86 4835.4,229 4844.9,223.75 4851.9,\ +214.39 4857,205.19", style=solid]; type [height=0.5, - pos="3273.4,178", + pos="5001.4,178", width=0.86659]; "disease or phenotypic feature to genetic inheritance association" -> type [color=blue, label=type, - lp="3305.4,221.5", - pos="e,3283.3,195.52 2200.2,251.76 2236.3,249.94 2273.4,248.26 2308.4,247 2335.5,246.02 3264.4,248.33 3283.4,229 3289.6,222.67 3289.4,\ -213.62 3286.9,204.97", + lp="5019.4,221.5", + pos="e,5004.1,195.99 3177.1,251.63 3213.8,249.8 3251.7,248.14 3287.4,247 3311.1,246.24 4976.6,244.65 4994.4,229 5000.9,223.32 5003.4,\ +214.65 5004.1,206.12", style=solid]; category [height=0.5, - pos="3374.4,178", + pos="5102.4,178", width=1.4263]; "disease or phenotypic feature to genetic inheritance association" -> category [color=blue, label=category, - lp="3378.9,221.5", - pos="e,3363.3,195.85 2200.2,251.73 2236.3,249.92 2273.4,248.25 2308.4,247 2364.9,244.99 3273.5,251.35 3325.4,229 3337.8,223.67 3348.6,\ -213.57 3357,203.83", + lp="5097.9,221.5", + pos="e,5087.7,195.48 3177.1,251.62 3213.8,249.79 3251.7,248.14 3287.4,247 3336,245.45 4993.5,245.26 5039.4,229 5054.6,223.6 5069,212.84 \ +5080.1,202.68", style=solid]; predicate [height=0.5, - pos="3498.4,178", + pos="5226.4,178", width=1.5165]; "disease or phenotypic feature to genetic inheritance association" -> predicate [color=blue, label=predicate, - lp="3482.4,221.5", - pos="e,3478.4,195.01 2199.8,251.71 2236,249.9 2273.3,248.23 2308.4,247 2369.8,244.85 3355.3,245.78 3414.4,229 3434.3,223.34 3454.3,211.72 \ -3469.8,201.1", + lp="5204.4,221.5", + pos="e,5204.7,194.58 3176.7,251.63 3213.5,249.79 3251.6,248.13 3287.4,247 3389.9,243.75 5034.1,254.53 5133.4,229 5155.8,223.25 5178.7,\ +211.04 5196.1,200.13", style=solid]; object [height=0.5, pos="1470.4,91", width=1.0832]; "disease or phenotypic feature to genetic inheritance association" -> object [color=blue, label=object, - lp="3592.4,178", - pos="e,1509.6,92.524 2199.4,251.69 2235.7,249.87 2273.1,248.21 2308.4,247 2375.7,244.7 3456.9,251.48 3520.4,229 3554.2,217.01 3587.4,\ -185.79 3562.4,160 3525.7,122.08 1832.1,96.976 1519.7,92.662", + lp="5320.4,178", + pos="e,1509.6,91.936 3176.7,251.61 3213.5,249.77 3251.6,248.12 3287.4,247 3341.7,245.3 5190.6,245.35 5242.4,229 5278,217.76 5316.6,186.65 \ +5290.4,160 5221.1,89.43 1961.9,91.338 1519.8,91.922", style=solid]; subject -> object [label=relation, lp="1469.4,134.5", @@ -242,23 +355,23 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2355.4,265", + pos="3334.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2486.4,265", + pos="3465.4,265", width=2.0762]; "disease or phenotypic feature to genetic inheritance association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2657.4,265", + pos="3636.4,265", width=2.1665]; object -> relation [pos="e,1428.2,35.54 1457.9,73.889 1451,64.939 1442.2,53.617 1434.4,43.584", style=dotted]; "disease or phenotypic feature to genetic inheritance association_object" [color=blue, height=0.5, label="genetic inheritance", - pos="2854.4,265", + pos="3833.4,265", width=2.7984]; } diff --git a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg index 401e517e8f..de13a7f003 100644 --- a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg +++ b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease or phenotypic feature to genetic inheritance association - -disease or phenotypic feature to genetic inheritance association + +disease or phenotypic feature to genetic inheritance association @@ -24,9 +24,9 @@ disease or phenotypic feature to genetic inheritance association->association - + -is_a +is_a @@ -37,9 +37,9 @@ disease or phenotypic feature to genetic inheritance association->disease or phenotypic feature to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ disease or phenotypic feature to genetic inheritance association->id - - -id + + +id @@ -63,9 +63,9 @@ disease or phenotypic feature to genetic inheritance association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ disease or phenotypic feature to genetic inheritance association->name - - -name + + +name @@ -89,9 +89,9 @@ disease or phenotypic feature to genetic inheritance association->description - - -description + + +description @@ -102,9 +102,9 @@ disease or phenotypic feature to genetic inheritance association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ disease or phenotypic feature to genetic inheritance association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ disease or phenotypic feature to genetic inheritance association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ disease or phenotypic feature to genetic inheritance association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ disease or phenotypic feature to genetic inheritance association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ disease or phenotypic feature to genetic inheritance association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ disease or phenotypic feature to genetic inheritance association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ disease or phenotypic feature to genetic inheritance association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ disease or phenotypic feature to genetic inheritance association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ disease or phenotypic feature to genetic inheritance association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ disease or phenotypic feature to genetic inheritance association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ disease or phenotypic feature to genetic inheritance association->original predicate - - -original predicate + + +original predicate @@ -258,110 +258,253 @@ disease or phenotypic feature to genetic inheritance association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +disease or phenotypic feature to genetic inheritance association->subject category + + +subject category + + + +object category + +ontology class + + + +disease or phenotypic feature to genetic inheritance association->object category + + +object category + + + +subject closure + +string + + + +disease or phenotypic feature to genetic inheritance association->subject closure + + +subject closure + + + +object closure + +string + + + +disease or phenotypic feature to genetic inheritance association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +disease or phenotypic feature to genetic inheritance association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +disease or phenotypic feature to genetic inheritance association->object category closure + + +object category closure + + + +subject namespace + +string + + + +disease or phenotypic feature to genetic inheritance association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +disease or phenotypic feature to genetic inheritance association->object namespace + + +object namespace + + + +subject label closure + +string + + + +disease or phenotypic feature to genetic inheritance association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +disease or phenotypic feature to genetic inheritance association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +disease or phenotypic feature to genetic inheritance association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + disease or phenotypic feature to genetic inheritance association->type - - -type + + +type - + category - -category + +category - + disease or phenotypic feature to genetic inheritance association->category - - -category + + +category - + predicate - -predicate + +predicate - + disease or phenotypic feature to genetic inheritance association->predicate - - -predicate + + +predicate - + object object - + disease or phenotypic feature to genetic inheritance association->object - - -object + + +object - + subject->object relation - + relation relation - + subject->relation - + association_type - -string + +string - + association_category - -category type + +category type - + disease or phenotypic feature to genetic inheritance association_predicate - -predicate type + +predicate type - + object->relation - + disease or phenotypic feature to genetic inheritance association_object - -genetic inheritance + +genetic inheritance diff --git a/graphviz/disease_or_phenotypic_feature_to_location_association.gv b/graphviz/disease_or_phenotypic_feature_to_location_association.gv index 28c34a1baf..42c751d64d 100644 --- a/graphviz/disease_or_phenotypic_feature_to_location_association.gv +++ b/graphviz/disease_or_phenotypic_feature_to_location_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3681.4,283"]; + graph [bb="0,0,5396.4,283"]; node [label="\N"]; "disease or phenotypic feature to location association" [height=0.5, label="disease or phenotypic feature to location association", - pos="2010.4,265", + pos="3028.4,265", width=7.0771]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease or phenotypic feature to location association" -> association [label=is_a, - lp="666.39,221.5", - pos="e,106.72,190.7 1763.7,260.45 1491.5,255.87 1040.6,246.36 652.39,229 421.94,218.69 362.57,229.96 134.39,196 128.62,195.14 122.62,\ -194.05 116.66,192.84"]; + lp="664.39,221.5", + pos="e,106.72,190.7 2773.6,264.35 2338.2,264.04 1423.2,259.38 650.39,229 420.77,219.97 361.69,229.86 134.39,196 128.62,195.14 122.62,\ +194.05 116.66,192.83"]; "disease or phenotypic feature to entity association mixin" [height=0.5, pos="417.39,178", width=7.6188]; "disease or phenotypic feature to location association" -> "disease or phenotypic feature to entity association mixin" [label=uses, - lp="848.89,221.5", - pos="e,524.62,194.61 1757,263.07 1518.2,260.63 1150.6,252.84 832.39,229 731.56,221.44 617.55,207.3 534.58,195.98"]; + lp="846.89,221.5", + pos="e,521.5,194.66 2774.3,263.3 2279.2,261.37 1201,254.32 830.39,229 728.95,222.07 614.19,207.64 531.43,196.06"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "disease or phenotypic feature to location association" -> id [color=blue, label=id, - lp="972.39,221.5", - pos="e,777.11,189.95 1764.2,260.28 1505,255.55 1114.1,245.9 965.39,229 889.35,220.36 870.22,216.16 796.39,196 793.24,195.14 789.99,194.17 \ -786.75,193.15", + lp="967.39,221.5", + pos="e,777.37,190.01 2776,262.3 2263.9,258.47 1136,248 960.39,229 886.48,221 868.06,215.79 796.39,196 793.28,195.14 790.08,194.18 786.89,\ +193.17", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "disease or phenotypic feature to location association" -> iri [color=blue, label=iri, - lp="1098.4,221.5", - pos="e,881.99,190.23 1756.4,263.58 1571.3,261.03 1314.7,252.84 1090.4,229 1006,220.03 984.75,216.34 902.39,196 898.96,195.15 895.42,194.2 \ -891.89,193.19", + lp="1085.4,221.5", + pos="e,882.01,190.16 2773.6,264.76 2322,265.22 1398.4,261.91 1077.4,229 998.66,220.93 979.11,215.46 902.39,196 898.97,195.13 895.43,194.16 \ +891.9,193.14", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "disease or phenotypic feature to location association" -> name [color=blue, label=name, - lp="1210.4,221.5", - pos="e,1008.9,190.59 1774,258.26 1572.5,252.57 1299,242.71 1190.4,229 1130.6,221.46 1063.3,205.16 1018.6,193.22", + lp="1199.4,221.5", + pos="e,1007.6,191.06 2776.9,262.1 2307.9,258.14 1333.3,247.77 1179.4,229 1123,222.12 1059.8,205.98 1017.4,193.88", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "disease or phenotypic feature to location association" -> description [color=blue, label=description, - lp="1339.9,221.5", - pos="e,1159.5,193.16 1775.6,258 1604.6,252.57 1387.9,243.23 1299.4,229 1254.7,221.81 1205.2,207.7 1169.3,196.29", + lp="1330.9,221.5", + pos="e,1157.4,193.52 2775.8,262.58 2329,259.52 1432.8,250.74 1290.4,229 1247.9,222.51 1201.1,208.43 1167,196.86", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "disease or phenotypic feature to location association" -> "has attribute" [color=blue, label="has attribute", - lp="1499.4,221.5", - pos="e,1299.9,191.01 1770.3,258.92 1671.4,254.24 1555.9,245.44 1452.4,229 1402.9,221.13 1347.5,205.68 1309.6,194.03", + lp="1492.4,221.5", + pos="e,1298.4,191.41 2777.2,261.81 2363.9,257.7 1573,247.53 1445.4,229 1397.7,222.07 1344.7,206.59 1308.2,194.67", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "disease or phenotypic feature to location association" -> subject [color=blue, label=subject, - lp="1649.4,221.5", - pos="e,1449.8,191.45 1827.2,252.47 1762.6,247.07 1689.5,239.46 1623.4,229 1567.1,220.1 1503.7,205.16 1459.5,193.93", + lp="1657.4,221.5", + pos="e,1448.8,191.65 2774.5,263.44 2433.3,261.69 1845,254.86 1631.4,229 1571.6,221.76 1504.4,206.08 1458.5,194.2", style=solid]; predicate [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1665]; "disease or phenotypic feature to location association" -> predicate [color=blue, label=predicate, - lp="1767.4,221.5", - pos="e,1610,193.49 1864.1,250.23 1821.7,244.97 1775.5,238 1733.4,229 1694.6,220.7 1651.8,207.5 1619.6,196.75", + lp="1795.4,221.5", + pos="e,1612.3,193.17 2774,263.79 2461.5,262.34 1949.7,255.77 1761.4,229 1713.5,222.19 1660.4,207.8 1622.2,196.2", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "disease or phenotypic feature to location association" -> negated [color=blue, label=negated, - lp="1880.4,221.5", - pos="e,1743.5,191.48 1927.8,247.92 1903,242.55 1876,236.09 1851.4,229 1817.8,219.31 1780.6,205.77 1753.1,195.22", + lp="1939.4,221.5", + pos="e,1747,190.39 2777.5,261.84 2500.2,258.45 2071.6,249.92 1910.4,229 1856.6,222.02 1796.4,205.52 1756.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "disease or phenotypic feature to location association" -> qualifiers [color=blue, label=qualifiers, - lp="1972.9,221.5", - pos="e,1879.9,195.02 1974.8,247.03 1963.4,241.45 1950.8,235.11 1939.4,229 1922.5,219.92 1904,209.3 1888.6,200.19", + lp="2072.9,221.5", + pos="e,1895.3,193.2 2778,261.61 2532.6,258.09 2176.3,249.55 2039.4,229 1993.1,222.05 1941.8,207.75 1904.8,196.22", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "disease or phenotypic feature to location association" -> publications [color=blue, label=publications, - lp="2054.4,221.5", - pos="e,2010.4,196.18 2010.4,246.8 2010.4,235.16 2010.4,219.55 2010.4,206.24", + lp="2210.4,221.5", + pos="e,2045,193.08 2778.9,261.31 2567,257.64 2279.6,249.06 2166.4,229 2127.7,222.15 2085.4,208.15 2054.6,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,8 +127,8 @@ digraph { width=2.0943]; "disease or phenotypic feature to location association" -> "has evidence" [color=blue, label="has evidence", - lp="2171.9,221.5", - pos="e,2148.1,195.69 2062.7,247.2 2076,242.09 2090,235.97 2102.4,229 2115.7,221.48 2129.3,211.34 2140.5,202.15", + lp="2356.9,221.5", + pos="e,2200.8,194.09 2785.2,259.53 2613.3,254.97 2398.3,246.04 2310.4,229 2275.9,222.31 2238.4,209.1 2210.3,197.94", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -137,8 +137,8 @@ digraph { width=3.015]; "disease or phenotypic feature to location association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2335.9,221.5", - pos="e,2328.3,194.73 2123.9,248.83 2156,243.59 2190.7,236.97 2222.4,229 2255,220.77 2290.8,208.57 2318.8,198.28", + lp="2495.9,221.5", + pos="e,2384,195.95 2798.8,257.17 2645.4,251.46 2465.8,242.13 2431.4,229 2416.6,223.35 2402.5,212.89 2391.5,202.99", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -147,8 +147,8 @@ digraph { width=3.015]; "disease or phenotypic feature to location association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2571.4,221.5", - pos="e,2553.1,193.96 2201.8,253.09 2266.4,247.79 2338.8,240.08 2404.4,229 2451.7,221.01 2504.2,207.6 2543.5,196.68", + lp="2662.4,221.5", + pos="e,2579.2,195.77 2785.3,259.61 2682.9,255.18 2583.5,246.38 2567.4,229 2560,220.97 2564.2,211.37 2572,202.74", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -157,9 +157,8 @@ digraph { width=3.015]; "disease or phenotypic feature to location association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2837.9,221.5", - pos="e,2796.3,194.66 2188.2,252.09 2217,250.29 2246.5,248.53 2274.4,247 2450.3,237.34 2496.7,258.35 2670.4,229 2710.1,222.29 2753.6,209.16 \ -2786.4,198.04", + lp="2871.9,221.5", + pos="e,2789.2,194.17 2826.9,253.98 2798.6,248.6 2775.6,240.65 2765.4,229 2755,217.1 2764.7,206.69 2780.1,198.49", style=solid]; timepoint [color=blue, height=0.5, @@ -168,9 +167,8 @@ digraph { width=1.5346]; "disease or phenotypic feature to location association" -> timepoint [color=blue, label=timepoint, - lp="3013.4,221.5", - pos="e,3003.4,195.17 2184.7,251.85 2214.6,250.03 2245.4,248.32 2274.4,247 2349.2,243.59 2877.2,252.34 2948.4,229 2965.6,223.36 2982.4,\ -212.17 2995.4,201.8", + lp="3018.4,221.5", + pos="e,2997.6,194.47 2998.3,246.83 2992.3,241.89 2986.8,235.93 2983.4,229 2978.7,219.42 2983.1,209.79 2990.4,201.57", style=solid]; "original subject" [color=blue, height=0.5, @@ -179,9 +177,8 @@ digraph { width=1.0652]; "disease or phenotypic feature to location association" -> "original subject" [color=blue, label="original subject", - lp="3141.4,221.5", - pos="e,3114.7,193.99 2183.9,251.8 2214.1,249.98 2245.1,248.28 2274.4,247 2360.8,243.22 2969.6,253.8 3052.4,229 3072.1,223.11 3091.7,210.99 \ -3106.5,200.17", + lp="3132.4,221.5", + pos="e,3108.4,192.24 3043,246.75 3052.1,236.6 3064.3,223.86 3076.4,214 3083.6,208.17 3091.8,202.54 3099.7,197.56", style=solid]; "original predicate" [color=blue, height=0.5, @@ -190,47 +187,165 @@ digraph { width=1.5887]; "disease or phenotypic feature to location association" -> "original predicate" [color=blue, label="original predicate", - lp="3285.9,221.5", - pos="e,3236.5,195.81 2183.2,251.75 2213.6,249.92 2244.9,248.23 2274.4,247 2325.9,244.84 3154.5,250.41 3201.4,229 3213.1,223.67 3223,213.71 \ -3230.5,204.07", + lp="3274.9,221.5", + pos="e,3231.2,195.85 3134.7,248.53 3153.1,243.68 3171.7,237.33 3188.4,229 3201.5,222.46 3214,212.32 3224.1,202.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3378.4,178", + pos="3360.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "original object" [color=blue, label="original object", - lp="3418.9,221.5", - pos="e,3374.7,196.04 2182.5,251.73 2213.1,249.89 2244.7,248.2 2274.4,247 2304.3,245.79 3328,244.97 3353.4,229 3361.8,223.68 3367.5,214.57 \ -3371.3,205.57", + lp="3402.9,221.5", + pos="e,3357.4,196.13 3242.5,255.23 3284.6,249.97 3321.1,241.76 3338.4,229 3346.1,223.36 3351.1,214.47 3354.4,205.74", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3493.4,178", + width=2.1304]; + "disease or phenotypic feature to location association" -> "subject category" [color=blue, + label="subject category", + lp="3533.9,221.5", + pos="e,3486.3,195.95 3212.6,252.54 3324.2,245.01 3447.2,235.4 3458.4,229 3468,223.47 3475.7,214.06 3481.3,204.89", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3664.4,178", + width=2.1304]; + "disease or phenotypic feature to location association" -> "object category" [color=blue, + label="object category", + lp="3679.9,221.5", + pos="e,3647.9,195.71 3208.7,252.26 3236.7,250.47 3265.3,248.67 3292.4,247 3360.2,242.82 3533.6,252.28 3597.4,229 3613.1,223.26 3628.3,\ +212.54 3640.2,202.49", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3797.4,178", + width=1.0652]; + "disease or phenotypic feature to location association" -> "subject closure" [color=blue, + label="subject closure", + lp="3815.9,221.5", + pos="e,3781.6,194.7 3205.2,252.03 3234.3,250.22 3264.2,248.48 3292.4,247 3342,244.4 3693.2,247.25 3739.4,229 3747.3,225.89 3761.7,213.47 \ +3774.2,201.79", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3893.4,178", + width=1.0652]; + "disease or phenotypic feature to location association" -> "object closure" [color=blue, + label="object closure", + lp="3935.4,221.5", + pos="e,3890.9,196.39 3203.4,251.91 3233.1,250.09 3263.6,248.37 3292.4,247 3324.6,245.46 3845.8,247.26 3872.4,229 3880.2,223.65 3885.1,\ +214.82 3888.2,206.06", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4026.4,178", + width=2.1304]; + "disease or phenotypic feature to location association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4093.9,221.5", + pos="e,4018.7,196.2 3202.7,251.83 3232.6,250.01 3263.4,248.31 3292.4,247 3331.1,245.26 3955,246.88 3989.4,229 3999.6,223.71 4007.7,214.22 \ +4013.6,204.92", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4215.4,178", + width=2.1304]; + "disease or phenotypic feature to location association" -> "object category closure" [color=blue, + label="object category closure", + lp="4283.9,221.5", + pos="e,4210.1,196.12 3201.2,251.77 3231.6,249.94 3262.9,248.25 3292.4,247 3342,244.91 4142.5,253.88 4185.4,229 4194.5,223.73 4201.2,214.5 \ +4205.8,205.39", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4405.4,178", + width=1.0652]; + "disease or phenotypic feature to location association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4455.4,221.5", + pos="e,4398.7,196.19 3200.5,251.73 3231.1,249.89 3262.7,248.2 3292.4,247 3322.3,245.79 4345,243.24 4371.4,229 4381.1,223.76 4388.6,214.41 \ +4394,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4564.4,178", + width=1.0652]; + "disease or phenotypic feature to location association" -> "object namespace" [color=blue, + label="object namespace", + lp="4608.4,221.5", + pos="e,4557,195.75 3200.2,251.7 3230.9,249.85 3262.6,248.18 3292.4,247 3326.7,245.65 4496.9,244.66 4527.4,229 4537.7,223.69 4545.9,214.01 \ +4551.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4715.4,178", + width=1.0652]; + "disease or phenotypic feature to location association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4768.4,221.5", + pos="e,4707.4,195.78 3199.8,251.68 3230.6,249.83 3262.4,248.16 3292.4,247 3330.8,245.51 4642,246.09 4676.4,229 4687.1,223.68 4695.8,213.86 \ +4702.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4886.4,178", + width=1.0652]; + "disease or phenotypic feature to location association" -> "object label closure" [color=blue, + label="object label closure", + lp="4934.9,221.5", + pos="e,4878.1,195.8 3199.8,251.64 3230.6,249.8 3262.4,248.14 3292.4,247 3335.5,245.36 4807.6,247.93 4846.4,229 4857.3,223.7 4866.1,213.89 \ +4872.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5048.4,178", + width=2.347]; + "disease or phenotypic feature to location association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5096.9,221.5", + pos="e,5039.8,196.3 3199.5,251.64 3230.4,249.79 3262.3,248.12 3292.4,247 3340,245.22 4965.5,249.87 5008.4,229 5019.1,223.78 5027.9,214.17 \ +5034.4,204.75", style=solid]; type [height=0.5, - pos="3466.4,178", + pos="5182.4,178", width=0.86659]; "disease or phenotypic feature to location association" -> type [color=blue, label=type, - lp="3496.4,221.5", - pos="e,3475.4,195.57 2182.5,251.69 2213.1,249.85 2244.7,248.18 2274.4,247 2291,246.34 3462.7,240.87 3474.4,229 3480.5,222.79 3480.7,213.88 \ -3478.6,205.31", + lp="5196.4,221.5", + pos="e,5183.2,196.19 3199.1,251.64 3230.1,249.78 3262.2,248.12 3292.4,247 3318.5,246.04 5150,245.25 5170.4,229 5177.2,223.54 5180.6,214.93 \ +5182.2,206.37", style=solid]; category [height=0.5, - pos="3567.4,178", + pos="5283.4,178", width=1.4263]; "disease or phenotypic feature to location association" -> category [color=blue, label=category, - lp="3569.9,221.5", - pos="e,3555.7,195.88 2182.2,251.7 2212.9,249.85 2244.6,248.18 2274.4,247 2308.9,245.64 3484.5,242.28 3516.4,229 3529.2,223.65 3540.6,\ -213.41 3549.3,203.58", + lp="5275.9,221.5", + pos="e,5267.8,195.26 3199.1,251.63 3230.1,249.77 3262.2,248.11 3292.4,247 3345.8,245.03 5165.7,246.08 5216.4,229 5232.6,223.54 5248.1,\ +212.51 5260.1,202.2", style=solid]; object [height=0.5, pos="1470.4,91", width=1.0832]; "disease or phenotypic feature to location association" -> object [color=blue, label=object, - lp="3659.4,178", - pos="e,1509.4,92.482 2182.2,251.67 2212.9,249.83 2244.6,248.16 2274.4,247 2311.3,245.56 3572.9,246.67 3605.4,229 3633.7,213.62 3649.8,\ -183.12 3627.4,160 3589.5,120.86 1837.8,96.685 1519.7,92.613", + lp="5374.4,178", + pos="e,1509.5,91.926 3199.1,251.62 3230.1,249.76 3262.2,248.11 3292.4,247 3348.4,244.95 5259.8,251.09 5311.4,229 5342.5,215.69 5367.1,\ +184.11 5343.4,160 5273.1,88.423 1965.3,91.209 1519.8,91.91", style=solid]; subject -> object [label=relation, lp="1469.4,134.5", @@ -243,18 +358,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2321.4,265", + pos="3339.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2452.4,265", + pos="3470.4,265", width=2.0762]; object -> relation [pos="e,1428.2,35.54 1457.9,73.889 1451,64.939 1442.2,53.617 1434.4,43.584", style=dotted]; "disease or phenotypic feature to location association_object" [color=blue, height=0.5, label="anatomical entity", - pos="2636.4,265", + pos="3654.4,265", width=2.5456]; } diff --git a/graphviz/disease_or_phenotypic_feature_to_location_association.svg b/graphviz/disease_or_phenotypic_feature_to_location_association.svg index a4ab58a9c6..ed94496406 100644 --- a/graphviz/disease_or_phenotypic_feature_to_location_association.svg +++ b/graphviz/disease_or_phenotypic_feature_to_location_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease or phenotypic feature to location association - -disease or phenotypic feature to location association + +disease or phenotypic feature to location association @@ -24,9 +24,9 @@ disease or phenotypic feature to location association->association - + -is_a +is_a @@ -37,9 +37,9 @@ disease or phenotypic feature to location association->disease or phenotypic feature to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ disease or phenotypic feature to location association->id - - -id + + +id @@ -63,9 +63,9 @@ disease or phenotypic feature to location association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ disease or phenotypic feature to location association->name - - -name + + +name @@ -89,9 +89,9 @@ disease or phenotypic feature to location association->description - - -description + + +description @@ -102,9 +102,9 @@ disease or phenotypic feature to location association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ disease or phenotypic feature to location association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ disease or phenotypic feature to location association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ disease or phenotypic feature to location association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ disease or phenotypic feature to location association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ disease or phenotypic feature to location association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ disease or phenotypic feature to location association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ disease or phenotypic feature to location association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ disease or phenotypic feature to location association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ disease or phenotypic feature to location association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ disease or phenotypic feature to location association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ disease or phenotypic feature to location association->original subject - - -original subject + + +original subject @@ -258,104 +258,247 @@ disease or phenotypic feature to location association->original predicate - - -original predicate + + +original predicate original object - -string + +string disease or phenotypic feature to location association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +disease or phenotypic feature to location association->subject category + + +subject category + + + +object category + +ontology class + + + +disease or phenotypic feature to location association->object category + + +object category + + + +subject closure + +string + + + +disease or phenotypic feature to location association->subject closure + + +subject closure + + + +object closure + +string + + + +disease or phenotypic feature to location association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +disease or phenotypic feature to location association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +disease or phenotypic feature to location association->object category closure + + +object category closure + + + +subject namespace + +string + + + +disease or phenotypic feature to location association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +disease or phenotypic feature to location association->object namespace + + +object namespace + + + +subject label closure + +string + + + +disease or phenotypic feature to location association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +disease or phenotypic feature to location association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +disease or phenotypic feature to location association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + disease or phenotypic feature to location association->type - - -type + + +type - + category - -category + +category - + disease or phenotypic feature to location association->category - - -category + + +category - + object object - + disease or phenotypic feature to location association->object - - -object + + +object - + subject->object relation - + relation relation - + subject->relation - + association_type - -string + +string - + association_category - -category type + +category type - + object->relation - + disease or phenotypic feature to location association_object - -anatomical entity + +anatomical entity diff --git a/graphviz/disease_to_exposure_event_association.gv b/graphviz/disease_to_exposure_event_association.gv index c5c8cc6e1e..62be02c51f 100644 --- a/graphviz/disease_to_exposure_event_association.gv +++ b/graphviz/disease_to_exposure_event_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,3981.7,283"]; + graph [bb="0,0,5668.7,283"]; node [label="\N"]; "disease to exposure event association" [height=0.5, label="disease to exposure event association", - pos="2088.4,265", + pos="3052.4,265", width=5.1815]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease to exposure event association" -> association [label=is_a, lp="669.39,221.5", - pos="e,106.48,190.8 1904.8,261.79 1632.1,257.99 1104,248.65 655.39,229 423.15,218.83 363.28,230.53 133.39,196 127.91,195.18 122.23,194.14 \ -116.57,192.98"]; + pos="e,106.48,190.8 2865.8,264.36 2462.4,264.45 1478.8,261.02 655.39,229 423.11,219.97 363.28,230.53 133.39,196 127.91,195.18 122.23,\ +194.14 116.57,192.98"]; "disease to entity association mixin" [height=0.5, pos="313.39,178", width=4.7482]; "disease to exposure event association" -> "disease to entity association mixin" [label=uses, - lp="911.89,221.5", - pos="e,430.57,191.15 1905.1,261.61 1670.8,257.87 1252.7,248.89 895.39,229 738.59,220.27 558.52,203.8 440.71,192.16"]; + lp="910.89,221.5", + pos="e,428.15,191.38 2867.5,262.57 2417.7,258.84 1275.8,247.77 894.39,229 736.82,221.25 555.8,204.41 438.26,192.41"]; "entity to exposure event association mixin" [height=0.5, pos="710.39,178", width=5.7773]; "disease to exposure event association" -> "entity to exposure event association mixin" [label=uses, - lp="1072.9,221.5", - pos="e,797.9,194.35 1902.1,263.81 1695.1,262.18 1351.2,255.22 1056.4,229 972.12,221.5 877.04,207.35 807.9,196.01"]; + lp="1070.9,221.5", + pos="e,795.58,194.45 2866.3,263.76 2439.9,262.71 1402.7,257.25 1054.4,229 969.83,222.14 874.4,207.74 805.54,196.14"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "disease to exposure event association" -> id [color=blue, label=id, - lp="1194.4,221.5", - pos="e,1003.4,190.01 1908.1,260.38 1686.1,255.33 1321.9,244.96 1187.4,229 1113.1,220.19 1094.5,215.87 1022.4,196 1019.3,195.14 1016.1,\ -194.18 1012.9,193.17", + lp="1189.4,221.5", + pos="e,1003.4,189.98 2867.4,262.48 2428.1,258.59 1346.3,247.28 1182.4,229 1110.2,220.95 1092.3,215.5 1022.4,196 1019.3,195.13 1016.1,\ +194.17 1012.9,193.15", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "disease to exposure event association" -> iri [color=blue, label=iri, - lp="1307.4,221.5", - pos="e,1108.3,190.23 1902.5,263.41 1742.2,261.07 1504.8,253.25 1299.4,229 1222.5,219.93 1203.4,215.19 1128.4,196 1125,195.14 1121.5,194.18 \ -1118.1,193.17", + lp="1296.4,221.5", + pos="e,1108.3,190.16 2865.6,264.63 2476.3,265.23 1589.1,262.7 1288.4,229 1216.2,220.91 1198.6,214.45 1128.4,196 1125,195.11 1121.5,194.14 \ +1118.1,193.12", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "disease to exposure event association" -> name [color=blue, label=name, - lp="1409.4,221.5", - pos="e,1232.8,191.29 1911.8,259.19 1738.4,253.74 1486.3,243.66 1389.4,229 1338.5,221.3 1281.7,205.93 1242.6,194.25", + lp="1400.4,221.5", + pos="e,1231.3,191.75 2867.2,262.65 2462.6,259.32 1524,249.5 1380.4,229 1331.9,222.08 1278.1,206.72 1240.8,194.84", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "disease to exposure event association" -> description [color=blue, label=description, - lp="1523.9,221.5", - pos="e,1377.9,194.13 1911,259.36 1762.3,254.44 1562.1,245.09 1483.4,229 1450.3,222.23 1414.4,209.18 1387.4,198.11", + lp="1516.9,221.5", + pos="e,1375.8,194.37 2866.5,263.41 2478.9,261.66 1609.3,254.86 1476.4,229 1444.7,222.84 1410.7,209.79 1385.1,198.56", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "disease to exposure event association" -> "has attribute" [color=blue, label="has attribute", - lp="1660.4,221.5", - pos="e,1517.6,193.33 1920.4,257.1 1807.8,251.43 1670,242.17 1613.4,229 1583.3,221.99 1550.9,208.73 1526.8,197.62", + lp="1655.4,221.5", + pos="e,1515.9,193.52 2866.6,263.35 2504.2,261.52 1728,254.62 1608.4,229 1579.1,222.73 1548,209.39 1524.9,198.06", style=solid]; subject [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.9318]; "disease to exposure event association" -> subject [color=blue, label=subject, - lp="1783.4,221.5", - pos="e,1661,194.08 1928.2,255.73 1873.5,250.63 1812.3,242.36 1757.4,229 1727.4,221.7 1695.1,209.01 1670.4,198.25", + lp="1782.4,221.5", + pos="e,1659.5,194.33 2867.5,262.55 2535.2,259.43 1862,250.52 1756.4,229 1726,222.8 1693.4,209.83 1668.9,198.66", style=solid]; predicate [color=blue, height=0.5, @@ -94,7 +94,7 @@ digraph { "disease to exposure event association" -> predicate [color=blue, label=predicate, lp="1861.4,221.5", - pos="e,1801.9,196.2 1936.9,254.5 1890.5,249.27 1846.6,241.25 1827.4,229 1818.5,223.33 1811.6,214.19 1806.5,205.27", + pos="e,1801.4,196.12 2866.7,263.23 2535.2,261.23 1871.7,254.09 1827.4,229 1818,223.67 1810.9,214.3 1805.8,205.1", style=solid]; object [color=blue, height=0.5, @@ -104,7 +104,7 @@ digraph { "disease to exposure event association" -> object [color=blue, label=object, lp="1940.4,178", - pos="e,1769,105.47 2031.6,247.72 1997.2,236.32 1953.3,219.01 1918.4,196 1899.5,183.54 1901.1,172.77 1882.4,160 1850.3,138.07 1810,120.64 \ + pos="e,1769,105.47 2870.3,260.97 2571.2,254.83 2000.9,237.76 1918.4,196 1898.2,185.78 1901.1,172.77 1882.4,160 1850.3,138.07 1810,120.64 \ 1778.5,108.92", style=solid]; negated [color=blue, @@ -114,8 +114,8 @@ digraph { width=1.2999]; "disease to exposure event association" -> negated [color=blue, label=negated, - lp="2087.4,221.5", - pos="e,2031.8,195.31 2074.2,246.8 2063.9,234.23 2049.7,217.01 2038.2,203.08", + lp="2242.4,221.5", + pos="e,2052.8,190.38 2871.7,260.47 2663.9,255.71 2335.8,245.82 2213.4,229 2160.7,221.75 2101.7,205.44 2062.5,193.41", style=solid]; qualifiers [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=2.1304]; "disease to exposure event association" -> qualifiers [color=blue, label=qualifiers, - lp="2166.9,221.5", - pos="e,2146.7,195.93 2104.6,246.79 2109.8,241.2 2115.4,234.91 2120.4,229 2127.1,221.01 2134.3,212.07 2140.5,203.97", + lp="2373.9,221.5", + pos="e,2200.9,193.28 2873.7,259.71 2697,254.65 2439.1,244.87 2340.4,229 2295.8,221.84 2246.5,207.79 2210.6,196.41", style=solid]; publications [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=1.7332]; "disease to exposure event association" -> publications [color=blue, label=publications, - lp="2283.4,221.5", - pos="e,2285.9,193.86 2147,247.89 2165.5,242.38 2186,235.86 2204.4,229 2228.8,219.91 2255.4,208.1 2276.6,198.24", + lp="2508.4,221.5", + pos="e,2350.1,193.26 2877.5,258.72 2733.4,253.41 2540.6,243.87 2464.4,229 2428.2,221.93 2388.6,208.25 2359.5,196.98", style=solid]; "has evidence" [color=blue, height=0.5, @@ -144,8 +144,8 @@ digraph { width=2.0943]; "disease to exposure event association" -> "has evidence" [color=blue, label="has evidence", - lp="2425.9,221.5", - pos="e,2436.5,193.96 2209.8,251.31 2248.9,245.94 2292.3,238.65 2331.4,229 2364,220.96 2399.5,208.31 2426.8,197.75", + lp="2649.9,221.5", + pos="e,2504.7,194.32 2869,261.57 2787,257.46 2689.5,248.36 2603.4,229 2572.5,222.06 2539.3,209.29 2514,198.39", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -154,8 +154,8 @@ digraph { width=3.015]; "disease to exposure event association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2612.9,221.5", - pos="e,2624,194.07 2222.2,252.43 2329.3,243.09 2463.7,231.16 2476.4,229 2523.1,221.05 2574.9,207.79 2613.9,196.92", + lp="2782.9,221.5", + pos="e,2684.8,196.41 2882.7,257.52 2815.6,252.63 2747.5,244.05 2718.4,229 2707.5,223.39 2698.2,213.9 2690.9,204.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -164,9 +164,8 @@ digraph { width=3.015]; "disease to exposure event association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2859.4,221.5", - pos="e,2855,193.66 2217.8,252.02 2240,250.18 2262.8,248.42 2284.4,247 2460.6,235.37 2506.3,252 2681.4,229 2737.4,221.65 2799.9,207.5 \ -2845.3,196.12", + lp="2949.4,221.5", + pos="e,2872.8,195.17 2915.3,252.72 2887.4,247.54 2863.6,240 2854.4,229 2846,218.96 2852.9,209.01 2864.3,200.67", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -175,9 +174,8 @@ digraph { width=3.015]; "disease to exposure event association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3137.9,221.5", - pos="e,3099.2,194.38 2215.9,251.83 2238.7,249.97 2262.2,248.26 2284.4,247 2434,238.52 2810.1,250.6 2958.4,229 3003.2,222.48 3052.6,208.89 \ -3089.2,197.52", + lp="3159.9,221.5", + pos="e,3079.9,192.66 3048.2,246.77 3046.8,236.38 3046.8,223.38 3053.4,214 3058,207.37 3064.1,202 3071,197.65", style=solid]; timepoint [color=blue, height=0.5, @@ -186,9 +184,8 @@ digraph { width=1.5346]; "disease to exposure event association" -> timepoint [color=blue, label=timepoint, - lp="3316.4,221.5", - pos="e,3308,194.99 2214.8,251.77 2238,249.89 2261.9,248.19 2284.4,247 2337.9,244.18 3197.1,244.54 3248.4,229 3267,223.36 3285.4,211.89 \ -3299.7,201.36", + lp="3321.4,221.5", + pos="e,3309.1,195.19 3189.2,252.76 3215.6,247.53 3242.4,239.95 3266.4,229 3274.1,225.48 3288.6,213.47 3301.4,202.1", style=solid]; "original subject" [color=blue, height=0.5, @@ -197,49 +194,170 @@ digraph { width=1.0652]; "disease to exposure event association" -> "original subject" [color=blue, label="original subject", - lp="3445.4,221.5", - pos="e,3420,194.04 2214.8,251.73 2237.9,249.86 2261.9,248.16 2284.4,247 2343.8,243.93 3298.2,245.42 3355.4,229 3375.7,223.18 3396,211.07 \ -3411.5,200.22", + lp="3438.4,221.5", + pos="e,3416.3,192.7 3182.3,252 3258.2,244.5 3342.4,235.12 3359.4,229 3370.9,224.86 3372.1,220.57 3382.4,214 3390.6,208.79 3399.4,203.21 \ +3407.7,198.07", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3553.4,178", + pos="3552.4,178", width=1.5887]; "disease to exposure event association" -> "original predicate" [color=blue, label="original predicate", - lp="3590.9,221.5", - pos="e,3542.6,195.86 2214.6,251.71 2237.8,249.84 2261.8,248.15 2284.4,247 2352.1,243.57 3443.2,256.06 3505.4,229 3517.6,223.68 3528.3,\ -213.58 3536.4,203.84", + lp="3578.9,221.5", + pos="e,3535.8,195.4 3184.7,252.28 3206,250.46 3227.8,248.65 3248.4,247 3303,242.63 3443.7,249.95 3494.4,229 3502.1,225.82 3516.1,213.82 \ +3528.4,202.37", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3703.4,178", + pos="3666.4,178", width=1.0652]; "disease to exposure event association" -> "original object" [color=blue, label="original object", - lp="3730.9,221.5", - pos="e,3693.6,195.84 2214.3,251.7 2237.6,249.82 2261.7,248.13 2284.4,247 2322.5,245.1 3623.6,244.76 3658.4,229 3670.1,223.71 3680,213.75 \ -3687.6,204.11", + lp="3708.9,221.5", + pos="e,3663.6,196.36 3181.8,252.02 3204,250.18 3226.8,248.42 3248.4,247 3292.3,244.1 3608.1,253.9 3644.4,229 3652.2,223.62 3657.3,214.79 \ +3660.6,206.03", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3799.4,178", + width=2.1304]; + "disease to exposure event association" -> "subject category" [color=blue, + label="subject category", + lp="3840.9,221.5", + pos="e,3792.4,196.13 3180.7,251.92 3203.2,250.06 3226.5,248.33 3248.4,247 3277,245.26 3739.2,242.69 3764.4,229 3774.2,223.69 3781.8,214.33 \ +3787.4,205.12", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3970.4,178", + width=2.1304]; + "disease to exposure event association" -> "object category" [color=blue, + label="object category", + lp="3987.9,221.5", + pos="e,3954.5,195.64 3179.9,251.84 3202.7,249.98 3226.2,248.26 3248.4,247 3321.2,242.85 3835.6,253.17 3904.4,229 3920.2,223.46 3935.2,\ +212.65 3946.9,202.5", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4103.4,178", + width=1.0652]; + "disease to exposure event association" -> "subject closure" [color=blue, + label="subject closure", + lp="4121.9,221.5", + pos="e,4088,194.74 3179.4,251.79 3202.3,249.93 3226.1,248.22 3248.4,247 3292.7,244.58 4005.1,245.09 4046.4,229 4054.2,225.95 4068.4,213.53 \ +4080.6,201.84", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4199.4,178", + width=1.0652]; + "disease to exposure event association" -> "object closure" [color=blue, + label="object closure", + lp="4241.4,221.5", + pos="e,4197,196.43 3179.1,251.76 3202.1,249.89 3226,248.19 3248.4,247 3274.2,245.63 4157,243.51 4178.4,229 4186.2,223.7 4191.1,214.88 \ +4194.2,206.11", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4332.4,178", + width=2.1304]; + "disease to exposure event association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4399.9,221.5", + pos="e,4324.8,196.23 3178.8,251.74 3202,249.86 3225.9,248.17 3248.4,247 3277.4,245.49 4269.5,242.31 4295.4,229 4305.6,223.76 4313.7,214.27 \ +4319.7,204.96", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4521.4,178", + width=2.1304]; + "disease to exposure event association" -> "object category closure" [color=blue, + label="object category closure", + lp="4589.9,221.5", + pos="e,4516.1,196.14 3178.6,251.71 3201.8,249.83 3225.8,248.14 3248.4,247 3282.9,245.26 4461.5,246.23 4491.4,229 4500.5,223.75 4507.2,\ +214.53 4511.9,205.42", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4711.4,178", + width=1.0652]; + "disease to exposure event association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4761.4,221.5", + pos="e,4704.8,196.21 3178.3,251.69 3201.6,249.81 3225.7,248.13 3248.4,247 3288,245.03 4642.4,247.79 4677.4,229 4687.1,223.78 4694.6,214.43 \ +4700,205.22", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4870.4,178", + width=1.0652]; + "disease to exposure event association" -> "object namespace" [color=blue, + label="object namespace", + lp="4914.4,221.5", + pos="e,4863,195.76 3178,251.69 3201.4,249.8 3225.6,248.12 3248.4,247 3292.4,244.85 4794.2,249.04 4833.4,229 4843.7,223.71 4851.9,214.03 \ +4857.9,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="5021.4,178", + width=1.0652]; + "disease to exposure event association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5074.4,221.5", + pos="e,5013.4,195.79 3178,251.67 3201.4,249.79 3225.6,248.1 3248.4,247 3296.5,244.67 4939.2,250.36 4982.4,229 4993.1,223.69 5001.8,213.88 \ +5008.2,204.34", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5192.4,178", + width=1.0652]; + "disease to exposure event association" -> "object label closure" [color=blue, + label="object label closure", + lp="5240.9,221.5", + pos="e,5184.1,195.81 3178,251.66 3201.4,249.77 3225.6,248.09 3248.4,247 3301.2,244.46 5104.8,252.14 5152.4,229 5163.3,223.71 5172.1,213.9 \ +5178.7,204.36", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5354.4,178", + width=2.347]; + "disease to exposure event association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5402.9,221.5", + pos="e,5345.8,196.3 3177.8,251.66 3201.2,249.77 3225.5,248.09 3248.4,247 3305.7,244.27 5262.8,254.09 5314.4,229 5325.1,223.79 5333.9,\ +214.18 5340.4,204.76", style=solid]; type [height=0.5, - pos="3829.4,178", + pos="5516.4,178", width=0.86659]; "disease to exposure event association" -> type [color=blue, label=type, - lp="3822.4,221.5", - pos="e,3820.5,195.34 2214.3,251.68 2237.6,249.8 2261.7,248.12 2284.4,247 2326.1,244.95 3748.6,246.63 3786.4,229 3798,223.61 3807.6,213.45 \ -3814.8,203.68", + lp="5511.4,221.5", + pos="e,5508.1,195.81 3177.8,251.65 3201.2,249.76 3225.5,248.08 3248.4,247 3279.3,245.54 5448.6,242.52 5476.4,229 5487.3,223.72 5496.1,\ +213.91 5502.7,204.36", style=solid]; category [height=0.5, - pos="3930.4,178", + pos="5617.4,178", width=1.4263]; "disease to exposure event association" -> category [color=blue, label=category, - lp="3908.9,221.5", - pos="e,3910,194.56 2214.3,251.68 2237.6,249.8 2261.7,248.11 2284.4,247 2370.9,242.76 3758.8,251.6 3842.4,229 3863.6,223.27 3885,211.23 \ -3901.5,200.41", + lp="5597.9,221.5", + pos="e,5597.2,194.83 3177.8,251.65 3201.2,249.76 3225.5,248.08 3248.4,247 3311.7,244.01 5470.2,245.75 5531.4,229 5552.1,223.34 5572.9,\ +211.43 5588.9,200.65", style=solid]; subject -> object [label=relation, lp="1712.4,134.5", @@ -254,11 +372,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2331.4,265", + pos="3295.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2462.4,265", + pos="3426.4,265", width=2.0762]; } diff --git a/graphviz/disease_to_exposure_event_association.svg b/graphviz/disease_to_exposure_event_association.svg index fe2a9bdd95..d88135a6d8 100644 --- a/graphviz/disease_to_exposure_event_association.svg +++ b/graphviz/disease_to_exposure_event_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease to exposure event association - -disease to exposure event association + +disease to exposure event association @@ -24,7 +24,7 @@ disease to exposure event association->association - + is_a @@ -37,9 +37,9 @@ disease to exposure event association->disease to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ disease to exposure event association->entity to exposure event association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ disease to exposure event association->id - - -id + + +id @@ -76,9 +76,9 @@ disease to exposure event association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ disease to exposure event association->name - - -name + + +name @@ -102,9 +102,9 @@ disease to exposure event association->description - - -description + + +description @@ -115,9 +115,9 @@ disease to exposure event association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ disease to exposure event association->subject - - -subject + + +subject @@ -141,8 +141,8 @@ disease to exposure event association->predicate - - + + predicate @@ -154,7 +154,7 @@ disease to exposure event association->object - + object @@ -167,9 +167,9 @@ disease to exposure event association->negated - - -negated + + +negated @@ -180,9 +180,9 @@ disease to exposure event association->qualifiers - - -qualifiers + + +qualifiers @@ -193,9 +193,9 @@ disease to exposure event association->publications - - -publications + + +publications @@ -206,9 +206,9 @@ disease to exposure event association->has evidence - - -has evidence + + +has evidence @@ -219,9 +219,9 @@ disease to exposure event association->knowledge source - - -knowledge source + + +knowledge source @@ -232,9 +232,9 @@ disease to exposure event association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -245,9 +245,9 @@ disease to exposure event association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -258,9 +258,9 @@ disease to exposure event association->timepoint - - -timepoint + + +timepoint @@ -271,98 +271,241 @@ disease to exposure event association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie disease to exposure event association->original predicate - - -original predicate + + +original predicate original object - -string + +string disease to exposure event association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +disease to exposure event association->subject category + + +subject category + + + +object category + +ontology class + + + +disease to exposure event association->object category + + +object category + + + +subject closure + +string + + + +disease to exposure event association->subject closure + + +subject closure + + + +object closure + +string + + + +disease to exposure event association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +disease to exposure event association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +disease to exposure event association->object category closure + + +object category closure + + + +subject namespace + +string + + + +disease to exposure event association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +disease to exposure event association->object namespace + + +object namespace + + + +subject label closure + +string + + + +disease to exposure event association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +disease to exposure event association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +disease to exposure event association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + disease to exposure event association->type - - -type + + +type - + category - -category + +category - + disease to exposure event association->category - - -category + + +category - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/disease_to_phenotypic_feature_association.gv b/graphviz/disease_to_phenotypic_feature_association.gv index 5cbff0425d..47759da97f 100644 --- a/graphviz/disease_to_phenotypic_feature_association.gv +++ b/graphviz/disease_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4955.4,283"]; + graph [bb="0,0,6639.4,283"]; node [label="\N"]; "disease to phenotypic feature association" [height=0.5, label="disease to phenotypic feature association", - pos="2980.4,265", + pos="3732.4,265", width=5.6328]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease to phenotypic feature association" -> association [label=is_a, lp="712.39,221.5", - pos="e,106.72,190.74 2777.7,263.82 2379.2,262.82 1465.8,257.32 698.39,229 447.47,219.74 382.85,232.32 134.39,196 128.61,195.16 122.61,\ + pos="e,106.72,190.74 3530.9,262.91 2945.7,259.55 1252.3,248.39 698.39,229 447.45,220.22 382.85,232.32 134.39,196 128.61,195.16 122.61,\ 194.07 116.66,192.87"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "disease to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="948.89,221.5", - pos="e,494.56,192.86 2779.4,262.39 2336.4,258.54 1287.3,247.71 932.39,229 786.11,221.29 619.05,205.65 504.76,193.91"]; + pos="e,493.43,192.91 3530.3,263.47 2975.7,261.68 1438.3,254.51 932.39,229 785.61,221.6 617.95,205.83 503.63,193.97"]; "disease to entity association mixin" [height=0.5, pos="780.39,178", width=4.7482]; "disease to phenotypic feature association" -> "disease to entity association mixin" [label=uses, lp="1104.9,221.5", - pos="e,855.33,194.23 2777.8,263.9 2359.2,263.1 1411,258.02 1088.4,229 1012.5,222.17 927.01,207.75 865.39,196.14"]; + pos="e,854.69,194.22 3530.7,263.05 2954.8,260.09 1328.6,249.97 1088.4,229 1012.2,222.35 926.42,207.83 864.76,196.15"]; id [color=blue, height=0.5, label=string, @@ -31,8 +31,8 @@ digraph { width=1.0652]; "disease to phenotypic feature association" -> id [color=blue, label=id, - lp="1225.4,221.5", - pos="e,1036.4,190 2777.3,264.55 2380.4,264.88 1514.6,261.66 1218.4,229 1144.9,220.9 1126.6,215.72 1055.4,196 1052.3,195.14 1049.1,194.18 \ + lp="1224.4,221.5", + pos="e,1036.4,190 3530.1,263.36 2973.3,261.29 1444,253.44 1217.4,229 1144.3,221.12 1126.2,215.65 1055.4,196 1052.3,195.14 1049.1,194.17 \ 1045.9,193.16", style=solid]; iri [color=blue, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "disease to phenotypic feature association" -> iri [color=blue, label=iri, - lp="1343.4,221.5", - pos="e,1141,190.15 2777.8,263.89 2401.7,263 1608.9,257.65 1335.4,229 1257.1,220.8 1237.7,215.39 1161.4,196 1158,195.13 1154.4,194.16 \ -1150.9,193.14", + lp="1341.4,221.5", + pos="e,1141.3,190.23 3530.3,263.08 2991.8,260.34 1548.4,251.02 1333.4,229 1256,221.07 1236.8,215.26 1161.4,196 1158,195.14 1154.5,194.18 \ +1151,193.17", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "disease to phenotypic feature association" -> name [color=blue, label=name, - lp="1455.4,221.5", - pos="e,1266.4,191.11 2777.5,264.58 2419.2,264.74 1688.7,260.96 1435.4,229 1380,222.01 1317.8,205.97 1276.1,193.93", + lp="1452.4,221.5", + pos="e,1266.2,191.3 3530.1,263.44 3007.2,261.64 1636.9,254.52 1432.4,229 1378,222.21 1317.1,206.27 1276,194.2", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "disease to phenotypic feature association" -> description [color=blue, label=description, - lp="1583.9,221.5", - pos="e,1415.3,193.6 2780.2,262.1 2413.8,258.18 1661.9,247.94 1543.4,229 1502.6,222.48 1457.8,208.57 1425,197.08", + lp="1579.9,221.5", + pos="e,1414.6,193.81 3529.8,264.04 3024,263.66 1732.2,259.66 1539.4,229 1499.6,222.68 1456.1,208.83 1424.2,197.3", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "disease to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1742.4,221.5", - pos="e,1556.6,191.69 2777.3,264.74 2469.1,264.8 1897.5,260.44 1695.4,229 1650.5,222.03 1600.9,206.88 1566.4,195.08", + lp="1735.4,221.5", + pos="e,1555.5,191.92 3530.1,263.7 3049.5,262.52 1866.5,256.8 1688.4,229 1645.5,222.31 1598.3,207.31 1565.3,195.48", style=solid]; predicate [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=2.1665]; "disease to phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="1896.4,221.5", - pos="e,1713.3,193.12 2778.5,263.08 2505.5,260.91 2033.2,253.59 1862.4,229 1814.5,222.1 1761.4,207.73 1723.2,196.15", + lp="1894.4,221.5", + pos="e,1712.4,193.16 3530.6,262.95 3080.6,260.2 2021.9,251.44 1860.4,229 1812.8,222.39 1760,207.91 1722.2,196.22", style=solid]; negated [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=1.2999]; "disease to phenotypic feature association" -> negated [color=blue, label=negated, - lp="2040.4,221.5", - pos="e,1848,190.33 2781.7,261.29 2542.4,257.24 2154.8,247.96 2011.4,229 1957.6,221.89 1897.4,205.41 1857.6,193.31", + lp="2036.4,221.5", + pos="e,1847.2,190.49 3531.5,262.33 3109,258.46 2154.7,247.76 2007.4,229 1954.8,222.3 1896.1,205.86 1857.2,193.65", style=solid]; qualifiers [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=2.1304]; "disease to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2172.9,221.5", - pos="e,1996.1,193.12 2782.8,260.84 2574,256.6 2258.6,247.36 2139.4,229 2093.6,221.94 2042.8,207.75 2006,196.28", + lp="2175.9,221.5", + pos="e,1996,193.12 3531.9,262.25 3135,258.4 2276.2,247.99 2142.4,229 2095.3,222.31 2043.1,207.84 2005.7,196.18", style=solid]; publications [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=1.7332]; "disease to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2310.4,221.5", - pos="e,2146.1,193.11 2784.8,260.17 2608.3,255.66 2362.1,246.46 2266.4,229 2228.1,222.01 2186.2,208.09 2155.6,196.71", + lp="2322.4,221.5", + pos="e,2147.2,192.77 3532,262.14 3162.1,258.27 2398.6,248.08 2278.4,229 2236.2,222.3 2189.8,207.8 2156.7,196.13", style=solid]; "has evidence" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=2.0943]; "disease to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2455.9,221.5", - pos="e,2301.6,194.09 2793,258.1 2655.3,252.71 2480.3,243.36 2409.4,229 2375.5,222.13 2338.7,208.99 2311,197.91", + lp="2482.9,221.5", + pos="e,2306,193.56 3529.5,264.95 3219,265.32 2640.6,261.39 2436.4,229 2394.7,222.39 2348.9,208.39 2315.5,196.89", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "disease to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2594.9,221.5", - pos="e,2484.7,196.09 2784.4,260.28 2685.1,256.11 2576,247.34 2530.4,229 2516.1,223.25 2502.6,212.88 2491.9,203.06", + lp="2639.9,221.5", + pos="e,2496.6,195.66 3531.6,262.38 3224.8,259.23 2665.4,250.59 2575.4,229 2551,223.14 2525.5,211.3 2505.6,200.62", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -143,8 +143,8 @@ digraph { width=3.015]; "disease to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2761.4,221.5", - pos="e,2679,195.74 2812.7,254.82 2743.6,249.29 2677.1,240.96 2666.4,229 2659,220.75 2663.5,211.17 2671.5,202.63", + lp="2813.4,221.5", + pos="e,2704.3,196.18 3530.7,263.09 3244,260.93 2749.7,253.64 2718.4,229 2711.4,223.47 2707.7,214.73 2705.8,206.08", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -153,8 +153,8 @@ digraph { width=3.015]; "disease to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2969.9,221.5", - pos="e,2887.2,193.89 2887.3,249 2878,244.02 2869.7,237.5 2863.4,229 2854.1,216.5 2863.2,206.22 2878,198.29", + lp="3022.9,221.5", + pos="e,2922.7,195.94 3531.8,262.26 3297,259.21 2937.4,250.97 2916.4,229 2909.8,222.07 2911.9,212.87 2916.9,204.26", style=solid]; timepoint [color=blue, height=0.5, @@ -163,8 +163,8 @@ digraph { width=1.5346]; "disease to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3128.4,221.5", - pos="e,3109.7,195.8 3039.2,247.71 3052,242.77 3065.1,236.59 3076.4,229 3086.5,222.2 3095.8,212.66 3103.3,203.73", + lp="3181.4,221.5", + pos="e,3125.3,196.37 3532.6,261.84 3375.6,258.52 3178.4,250.14 3146.4,229 3138.2,223.58 3132.6,214.62 3128.8,205.76", style=solid]; "original subject" [color=blue, height=0.5, @@ -173,8 +173,8 @@ digraph { width=1.0652]; "disease to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3245.4,221.5", - pos="e,3215.4,194.1 3099.1,250.35 3122.4,245.31 3146.1,238.42 3167.4,229 3176,225.2 3193,212.23 3207.6,200.45", + lp="3281.4,221.5", + pos="e,3224.4,195.9 3530.9,262.94 3398.8,260.07 3246.7,251.78 3225.4,229 3219.5,222.72 3219.3,213.94 3221.3,205.5", style=solid]; "original predicate" [color=blue, height=0.5, @@ -183,8 +183,8 @@ digraph { width=1.5887]; "disease to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3386.9,221.5", - pos="e,3337.6,195.9 3116.1,251.62 3200.9,243.5 3295.7,233.57 3304.4,229 3315.3,223.29 3324.6,213.59 3331.7,204.25", + lp="3410.9,221.5", + pos="e,3342.1,196.39 3545.1,258.09 3454.2,253.25 3361.6,244.53 3347.4,229 3341.9,222.96 3340.4,214.59 3340.8,206.43", style=solid]; "original object" [color=blue, height=0.5, @@ -193,162 +193,277 @@ digraph { width=1.0652]; "disease to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3514.9,221.5", - pos="e,3464,196.3 3124.1,252.26 3146.9,250.45 3170.3,248.64 3192.4,247 3221.5,244.83 3433,248.89 3454.4,229 3460.5,223.29 3463.1,214.86 \ -3463.8,206.55", + lp="3543.9,221.5", + pos="e,3467.6,196.15 3584.6,252.6 3545.1,247.33 3508.8,239.76 3492.4,229 3483.6,223.26 3476.9,214.11 3472,205.2", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3594.4,178", + width=2.1304]; + "disease to phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3666.9,221.5", + pos="e,3594.7,196.4 3637.3,249.1 3626.2,244.14 3615.8,237.6 3607.4,229 3601.5,222.97 3598.2,214.6 3596.3,206.44", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3765.4,178", + width=2.1304]; + "disease to phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3788.9,221.5", + pos="e,3745.6,195.74 3729.8,246.74 3729,236.82 3729.3,224.32 3733.4,214 3734.9,210.32 3736.9,206.79 3739.3,203.48", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3898.4,178", + width=1.0652]; + "disease to phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="3918.9,221.5", + pos="e,3884.7,194.97 3800.5,248.03 3815.5,243.08 3830.9,236.81 3844.4,229 3856.6,221.93 3868.3,211.65 3877.7,202.25", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "disease to phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4037.4,221.5", + pos="e,3992.6,196.43 3891.8,253.8 3929,248.62 3961.9,240.79 3976.4,229 3983.4,223.3 3987.7,214.67 3990.3,206.17", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4127.4,178", + width=2.1304]; + "disease to phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4195.9,221.5", + pos="e,4119.7,196.39 3878.6,252.51 3973.7,244.58 4081.8,234.51 4091.4,229 4101,223.48 4108.7,214.25 4114.5,205.21", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4319.4,178", + width=2.1304]; + "disease to phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4386.9,221.5", + pos="e,4313.3,196.03 3874,252.1 3897.5,250.28 3921.6,248.51 3944.4,247 3982.5,244.47 4254.4,248.19 4287.4,229 4296.7,223.61 4303.7,214.36 \ +4308.7,205.27", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4509.4,178", + width=1.0652]; + "disease to phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4559.4,221.5", + pos="e,4502.4,196.14 3871.7,251.91 3896,250.07 3920.9,248.34 3944.4,247 3973.8,245.32 4448.5,243.05 4474.4,229 4484.2,223.7 4491.8,214.33 \ +4497.4,205.13", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4668.4,178", + width=1.0652]; + "disease to phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4712.4,221.5", + pos="e,4661,195.7 3870.9,251.82 3895.4,249.97 3920.6,248.26 3944.4,247 3982.5,244.97 4597.5,246.63 4631.4,229 4641.7,223.63 4649.9,213.94 \ +4655.9,204.51", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4819.4,178", + width=1.0652]; + "disease to phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4872.4,221.5", + pos="e,4811.4,195.74 3870.3,251.77 3895,249.91 3920.4,248.22 3944.4,247 3990.8,244.64 4738.9,249.83 4780.4,229 4791.1,223.63 4799.7,213.81 \ +4806.1,204.28", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4958.4,178", + width=1.0652]; + "disease to phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5028.9,221.5", + pos="e,4960.7,196.01 3869.7,251.74 3894.6,249.87 3920.2,248.18 3944.4,247 3972.3,245.63 4929.3,247.32 4950.4,229 4956.9,223.35 4959.6,\ +214.68 4960.5,206.14", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5099.4,178", + width=2.347]; + "disease to phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5178.9,221.5", + pos="e,5106.2,196.1 3869.4,251.71 3894.4,249.84 3920.1,248.16 3944.4,247 3976.5,245.46 5079.8,251.92 5102.4,229 5108.3,223.01 5109.3,\ +214.41 5108.3,206.03", style=solid]; type [height=0.5, - pos="3549.4,178", + pos="5233.4,178", width=0.86659]; "disease to phenotypic feature association" -> type [color=blue, label=type, - lp="3591.4,221.5", - pos="e,3563.7,194.16 3121.5,252.04 3145.1,250.22 3169.5,248.47 3192.4,247 3213.4,245.66 3555.9,244.22 3570.4,229 3577.4,221.67 3574.8,\ -211.66 3569.4,202.53", + lp="5273.4,221.5", + pos="e,5246.9,194.33 3869.2,251.69 3894.2,249.83 3920.1,248.14 3944.4,247 3962.5,246.15 5239.6,241.94 5252.4,229 5259.3,221.96 5257.2,\ +212.12 5252.4,203.04", style=solid]; category [height=0.5, - pos="3650.4,178", + pos="5334.4,178", width=1.4263]; "disease to phenotypic feature association" -> category [color=blue, label=category, - lp="3660.9,221.5", - pos="e,3642.1,196.15 3120.9,252 3144.7,250.17 3169.3,248.42 3192.4,247 3238.9,244.14 3570,250.34 3611.4,229 3621.8,223.65 3630.3,214.15 \ -3636.6,204.85", + lp="5344.9,221.5", + pos="e,5325.8,195.8 3869.2,251.69 3894.2,249.82 3920.1,248.14 3944.4,247 3981.8,245.25 5259.6,245.26 5293.4,229 5304.4,223.71 5313.4,\ +213.89 5320.2,204.35", style=solid]; subject [height=0.5, - pos="3764.4,178", + pos="5448.4,178", width=1.2277]; "disease to phenotypic feature association" -> subject [color=blue, label=subject, - lp="3751.4,221.5", - pos="e,3748.7,194.87 3120,251.92 3144.1,250.08 3169,248.36 3192.4,247 3248.3,243.76 3643.5,247.42 3696.4,229 3713,223.23 3728.9,211.92 \ -3741.2,201.51", + lp="5435.4,221.5", + pos="e,5432.8,195 3869.2,251.67 3894.2,249.8 3920.1,248.13 3944.4,247 4024.1,243.31 5304.7,254.35 5380.4,229 5397,223.42 5413,212.12 \ +5425.3,201.67", style=solid]; object [height=0.5, - pos="3807.4,91", + pos="5491.4,91", width=1.0832]; "disease to phenotypic feature association" -> object [color=blue, label=object, - lp="3850.4,178", - pos="e,3820.8,108.09 3119.5,251.86 3143.8,250.02 3168.8,248.31 3192.4,247 3257.8,243.38 3720.7,253.67 3781.4,229 3822.5,212.28 3825.2,\ -186.07 3830.4,142 3831.2,135.38 3832.3,133.39 3830.4,127 3829.4,123.55 3827.9,120.13 3826.1,116.85", + lp="5534.4,178", + pos="e,5504.8,108.09 3868.9,251.68 3894,249.8 3920,248.12 3944.4,247 3986.6,245.06 5426.1,244.55 5465.4,229 5506.7,212.67 5509.2,186.07 \ +5514.4,142 5515.2,135.38 5516.3,133.39 5514.4,127 5513.4,123.55 5511.9,120.13 5510.1,116.85", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3991.4,178", + pos="5675.4,178", width=2.3651]; "disease to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3979.4,221.5", - pos="e,3958.9,194.69 3118.9,251.83 3143.4,249.99 3168.6,248.27 3192.4,247 3340.2,239.08 3713.1,257.44 3858.4,229 3889.9,222.82 3923.9,\ -209.97 3949.5,198.85", + lp="5663.4,221.5", + pos="e,5643.2,194.72 3868.9,251.67 3894,249.79 3920,248.12 3944.4,247 4033.1,242.95 5455.1,245.37 5542.4,229 5574.1,223.05 5608.1,210.13 \ +5633.8,198.91", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4170.4,178", + pos="5854.4,178", width=2.1123]; "disease to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4160.4,221.5", - pos="e,4141.6,194.75 3118,251.78 3142.8,249.92 3168.3,248.22 3192.4,247 3287.7,242.18 3958,248.84 4051.4,229 4079.7,222.98 4109.8,210.3 \ -4132.6,199.22", + lp="5844.4,221.5", + pos="e,5825.6,194.85 3868.6,251.66 3893.8,249.78 3919.9,248.11 3944.4,247 4043.8,242.52 5638,249.15 5735.4,229 5763.7,223.14 5793.8,210.46 \ +5816.6,199.33", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4300.4,178", + pos="5984.4,178", width=1.011]; "disease to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4307.9,221.5", - pos="e,4283.7,194.26 3117.7,251.73 3142.6,249.87 3168.2,248.18 3192.4,247 3249.7,244.2 4170.6,246.11 4225.4,229 4243.8,223.24 4261.9,\ -211.42 4275.7,200.72", + lp="5992.9,221.5", + pos="e,5967.7,194.31 3868.6,251.64 3893.8,249.77 3919.9,248.09 3944.4,247 3998.9,244.57 5857.2,245.06 5909.4,229 5927.8,223.32 5945.9,\ +211.5 5959.7,200.78", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="4428.4,178", + pos="6112.4,178", width=2.0401]; "disease to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="4435.4,221.5", - pos="e,4412.8,195.71 3117.4,251.71 3142.4,249.84 3168.1,248.16 3192.4,247 3257.4,243.9 4302,250.42 4363.4,229 4379,223.55 4393.8,212.75 \ -4405.4,202.58", + lp="6120.4,221.5", + pos="e,6097.1,195.74 3868.6,251.63 3893.8,249.76 3919.9,248.09 3944.4,247 4002.8,244.41 5993.2,248.26 6048.4,229 6063.9,223.6 6078.5,\ +212.8 6089.8,202.62", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="4564.4,178", + pos="6248.4,178", width=1.2277]; "disease to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="4552.4,221.5", - pos="e,4545.8,194.54 3117.2,251.7 3142.2,249.83 3168.1,248.14 3192.4,247 3264,243.63 4414.5,249.06 4483.4,229 4503,223.28 4522.6,211.41 \ -4537.6,200.67", + lp="6236.4,221.5", + pos="e,6230.1,194.57 3868.6,251.62 3893.8,249.75 3919.9,248.08 3944.4,247 4006.1,244.28 6109.1,246.27 6168.4,229 6187.8,223.34 6207.2,\ +211.47 6222,200.72", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="4670.4,178", + pos="6354.4,178", width=1.2277]; "disease to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="4655.9,221.5", - pos="e,4652.4,194.54 3117.2,251.68 3142.2,249.81 3168.1,248.13 3192.4,247 3270,243.39 4516.9,251.12 4591.4,229 4610.6,223.29 4629.7,211.42 \ -4644.3,200.68", + lp="6339.9,221.5", + pos="e,6336.4,194.57 3868.3,251.64 3893.6,249.75 3919.8,248.08 3944.4,247 4009.1,244.16 6213.3,247.27 6275.4,229 6294.7,223.33 6313.8,\ +211.47 6328.3,200.72", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="4774.4,178", + pos="6458.4,178", width=1.1735]; "disease to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="4770.4,221.5", - pos="e,4755.7,194.31 3116.9,251.68 3142,249.81 3168,248.13 3192.4,247 3275.6,243.17 4611.3,251.78 4691.4,229 4711.5,223.27 4731.7,211.28 \ -4747.2,200.48", + lp="6454.4,221.5", + pos="e,6439.7,194.34 3868.3,251.63 3893.6,249.75 3919.8,248.08 3944.4,247 4011.9,244.05 6310.4,247.32 6375.4,229 6395.6,223.31 6415.8,\ +211.33 6431.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4881.4,178", + pos="6565.4,178", width=1.1735]; "disease to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="4900.4,221.5", - pos="e,4866.9,195.47 3116.9,251.66 3142,249.79 3168,248.11 3192.4,247 3237.5,244.94 4776.9,244.28 4819.4,229 4834.5,223.58 4848.6,212.83 \ -4859.6,202.67", + lp="6584.4,221.5", + pos="e,6551.4,195 3868.3,251.62 3893.6,249.74 3919.8,248.07 3944.4,247 4015.4,243.91 6436.4,252.9 6503.4,229 6518.7,223.54 6533,212.56 \ +6544,202.28", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3239.4,265", + pos="3991.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3370.4,265", + pos="4122.4,265", width=2.0762]; subject -> object [label=relation, - lp="3802.4,134.5", - pos="e,3789.5,107.23 3765.5,159.55 3766.7,149.57 3769.2,137.07 3774.4,127 3776.6,122.68 3779.5,118.52 3782.7,114.66"]; + lp="5486.4,134.5", + pos="e,5473.5,107.23 5449.5,159.55 5450.7,149.57 5453.2,137.07 5458.4,127 5460.6,122.68 5463.5,118.52 5466.7,114.66"]; relation [height=0.5, - pos="3752.4,18", + pos="5436.4,18", width=1.2999]; - subject -> relation [pos="e,3753.7,36.188 3763.1,159.79 3761,132.48 3757,78.994 3754.5,46.38", + subject -> relation [pos="e,5437.7,36.188 5447.1,159.79 5445,132.48 5441,78.994 5438.5,46.38", style=dotted]; "disease to phenotypic feature association_subject" [color=blue, height=0.5, label=disease, - pos="3508.4,265", + pos="4260.4,265", width=1.2638]; - object -> relation [pos="e,3765.2,35.54 3794.9,73.889 3788,64.939 3779.2,53.617 3771.4,43.584", + object -> relation [pos="e,5449.2,35.54 5478.9,73.889 5472,64.939 5463.2,53.617 5455.4,43.584", style=dotted]; "disease to phenotypic feature association_object" [color=blue, height=0.5, label="phenotypic feature", - pos="3670.4,265", + pos="4422.4,265", width=2.7442]; } diff --git a/graphviz/disease_to_phenotypic_feature_association.svg b/graphviz/disease_to_phenotypic_feature_association.svg index 32a9bdeacc..988ed9d807 100644 --- a/graphviz/disease_to_phenotypic_feature_association.svg +++ b/graphviz/disease_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease to phenotypic feature association - -disease to phenotypic feature association + +disease to phenotypic feature association @@ -24,7 +24,7 @@ disease to phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ disease to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,8 +50,8 @@ disease to phenotypic feature association->disease to entity association mixin - - + + uses @@ -63,9 +63,9 @@ disease to phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ disease to phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ disease to phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ disease to phenotypic feature association->description - - -description + + +description @@ -115,9 +115,9 @@ disease to phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ disease to phenotypic feature association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ disease to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ disease to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ disease to phenotypic feature association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ disease to phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ disease to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ disease to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ disease to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ disease to phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ disease to phenotypic feature association->original subject - - -original subject + + +original subject @@ -258,9 +258,9 @@ disease to phenotypic feature association->original predicate - - -original predicate + + +original predicate @@ -271,214 +271,357 @@ disease to phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +disease to phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +disease to phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +disease to phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +disease to phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +disease to phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +disease to phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +disease to phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +disease to phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +disease to phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +disease to phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +disease to phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + disease to phenotypic feature association->type - - -type + + +type - + category - -category + +category - + disease to phenotypic feature association->category - - -category + + +category - + subject - -subject + +subject - + disease to phenotypic feature association->subject - - -subject + + +subject - + object - -object + +object - + disease to phenotypic feature association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + disease to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + disease to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + disease to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier - + sex qualifier - -biological sex + +biological sex - + disease to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier - + has count - -integer + +integer - + disease to phenotypic feature association->has count - - -has count + + +has count - + has total - -integer + +integer - + disease to phenotypic feature association->has total - - -has total + + +has total - + has quotient - -double + +double - + disease to phenotypic feature association->has quotient - - -has quotient + + +has quotient - + has percentage - -double + +double - + disease to phenotypic feature association->has percentage - - -has percentage + + +has percentage - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + disease to phenotypic feature association_subject - -disease + +disease - + object->relation - - + + - + disease to phenotypic feature association_object - -phenotypic feature + +phenotypic feature diff --git a/graphviz/drug_to_gene_association.gv b/graphviz/drug_to_gene_association.gv index d315ebc638..d9a14e4143 100644 --- a/graphviz/drug_to_gene_association.gv +++ b/graphviz/drug_to_gene_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3449.4,283"]; + graph [bb="0,0,5164.4,283"]; node [label="\N"]; "drug to gene association" [height=0.5, label="drug to gene association", - pos="1778.4,265", + pos="2796.4,265", width=3.4664]; association [height=0.5, pos="62.394,178", width=1.7332]; "drug to gene association" -> association [label=is_a, - lp="475.39,221.5", - pos="e,106.9,190.62 1653.9,263.75 1420,262.59 899.1,256.8 461.39,229 315.18,219.71 277.85,220.45 133.39,196 128.01,195.09 122.42,194 \ -116.85,192.82"]; + lp="466.39,221.5", + pos="e,107.28,190.69 2671.8,263.59 2251.9,261.98 890.16,254.86 452.39,229 310.11,220.59 273.9,219.98 133.39,196 128.08,195.09 122.58,\ +194.02 117.09,192.86"]; "drug to entity association mixin" [height=0.5, pos="301.39,178", width=4.4052]; "drug to gene association" -> "drug to entity association mixin" [label=uses, - lp="616.89,221.5", - pos="e,374.14,194.01 1654.5,262.45 1394.9,258.86 801.73,248.73 600.39,229 526.86,221.79 444.07,207.46 384.28,195.97"]; + lp="614.89,221.5", + pos="e,372.71,194.12 2671.5,264.49 2268.5,265.68 1005.2,266.26 598.39,229 524.93,222.27 442.23,207.77 382.79,196.11"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "drug to gene association" -> id [color=blue, label=id, - lp="740.39,221.5", - pos="e,545.11,189.95 1654.5,262.33 1417.6,258.72 908.24,248.87 733.39,229 657.35,220.36 638.22,216.16 564.39,196 561.24,195.14 557.99,\ -194.17 554.75,193.15", + lp="735.39,221.5", + pos="e,545.37,190.01 2671.9,263.21 2254.7,260.38 920.73,249.8 728.39,229 654.48,221 636.06,215.79 564.39,196 561.28,195.14 558.08,194.18 \ +554.89,193.17", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "drug to gene association" -> iri [color=blue, label=iri, - lp="866.39,221.5", - pos="e,649.99,190.23 1653.4,264.61 1476,264.25 1141.5,259.09 858.39,229 774.04,220.03 752.75,216.34 670.39,196 666.96,195.15 663.42,194.2 \ -659.89,193.19", + lp="853.39,221.5", + pos="e,650.01,190.16 2671.3,264.51 2299,265.59 1201.5,265.5 845.39,229 766.66,220.93 747.11,215.46 670.39,196 666.97,195.13 663.43,194.16 \ +659.9,193.14", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "drug to gene association" -> name [color=blue, label=name, - lp="978.39,221.5", - pos="e,776.9,190.59 1656.3,261.27 1461.7,256.51 1089.6,245.56 958.39,229 898.63,221.46 831.31,205.16 786.63,193.22", + lp="967.39,221.5", + pos="e,775.59,191.06 2672.1,263.12 2285.1,260.19 1117.2,249.7 947.39,229 891,222.12 827.78,205.98 785.37,193.88", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "drug to gene association" -> description [color=blue, label=description, - lp="1107.9,221.5", - pos="e,927.52,193.16 1656.3,261.23 1483.7,256.77 1177.1,246.64 1067.4,229 1022.7,221.81 973.18,207.7 937.27,196.29", + lp="1098.9,221.5", + pos="e,925.36,193.52 2672.1,263.38 2300.8,261.27 1216.2,253.1 1058.4,229 1015.9,222.51 969.07,208.43 935.04,196.86", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "drug to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="1267.4,221.5", - pos="e,1067.9,191.01 1654.4,262.94 1540.8,260.39 1368.4,252.5 1220.4,229 1170.9,221.13 1115.5,205.68 1077.6,194.03", + lp="1260.4,221.5", + pos="e,1066.4,191.41 2672.2,263 2324.2,259.94 1355.8,249.67 1213.4,229 1165.7,222.07 1112.7,206.59 1076.2,194.67", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "drug to gene association" -> subject [color=blue, label=subject, - lp="1417.4,221.5", - pos="e,1217.8,191.45 1664,257.67 1586.7,252.41 1482.5,243.41 1391.4,229 1335.1,220.1 1271.7,205.16 1227.5,193.93", + lp="1425.4,221.5", + pos="e,1216.8,191.65 2671.6,263.92 2376.8,263.25 1643.5,258.55 1399.4,229 1339.6,221.76 1272.4,206.08 1226.5,194.2", style=solid]; predicate [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1665]; "drug to gene association" -> predicate [color=blue, label=predicate, - lp="1535.4,221.5", - pos="e,1378,193.49 1674.1,255.06 1621.9,249.52 1557.9,241.1 1501.4,229 1462.6,220.7 1419.8,207.5 1387.6,196.75", + lp="1563.4,221.5", + pos="e,1380.3,193.17 2671.5,264.15 2396.8,263.9 1747,259.94 1529.4,229 1481.5,222.19 1428.4,207.8 1390.2,196.2", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "drug to gene association" -> negated [color=blue, label=negated, - lp="1648.4,221.5", - pos="e,1511.5,191.48 1706.7,250.26 1679.2,244.46 1647.6,237.15 1619.4,229 1585.8,219.31 1548.6,205.77 1521.1,195.22", + lp="1707.4,221.5", + pos="e,1515,190.39 2672,263.17 2422.2,261 1867.1,253.49 1678.4,229 1624.6,222.02 1564.4,205.52 1524.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "drug to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1740.9,221.5", - pos="e,1647.9,195.02 1743.8,247.56 1732.2,241.85 1719.1,235.3 1707.4,229 1690.5,219.92 1672,209.3 1656.6,200.19", + lp="1840.9,221.5", + pos="e,1663.3,193.2 2672,263.12 2444.6,260.92 1970.4,253.47 1807.4,229 1761.1,222.05 1709.8,207.75 1672.8,196.22", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "drug to gene association" -> publications [color=blue, label=publications, - lp="1822.4,221.5", - pos="e,1778.4,196.18 1778.4,246.8 1778.4,235.16 1778.4,219.55 1778.4,206.24", + lp="1978.4,221.5", + pos="e,1813,193.08 2671.9,263.06 2468.1,260.84 2072.2,253.42 1934.4,229 1895.7,222.15 1853.4,208.15 1822.6,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,8 +127,8 @@ digraph { width=2.0943]; "drug to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1939.9,221.5", - pos="e,1916.1,195.69 1827.9,248.29 1842,242.98 1857.1,236.47 1870.4,229 1883.7,221.48 1897.3,211.34 1908.5,202.15", + lp="2124.9,221.5", + pos="e,1968.8,194.09 2672.9,262.22 2498.4,258.98 2188.6,250.36 2078.4,229 2043.9,222.31 2006.4,209.1 1978.3,197.94", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -137,8 +137,8 @@ digraph { width=3.015]; "drug to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2103.9,221.5", - pos="e,2096.3,194.73 1868.6,252.5 1906.5,246.79 1950.9,238.96 1990.4,229 2023,220.77 2058.8,208.57 2086.8,198.28", + lp="2263.9,221.5", + pos="e,2152,195.95 2674.9,260.79 2513.2,255.92 2242.5,245.44 2199.4,229 2184.6,223.35 2170.5,212.89 2159.5,202.99", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -147,9 +147,8 @@ digraph { width=3.015]; "drug to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2339.4,221.5", - pos="e,2321.6,194.12 1866.3,252.13 1881.6,250.26 1897.5,248.46 1912.4,247 2027.7,235.71 2058,247.18 2172.4,229 2219.9,221.45 2272.7,207.95 \ -2311.9,196.88", + lp="2430.4,221.5", + pos="e,2347.2,195.77 2672.2,263.09 2543.5,260.83 2357.9,253.32 2335.4,229 2328,220.97 2332.2,211.37 2340,202.74", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -158,9 +157,8 @@ digraph { width=3.015]; "drug to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2606.9,221.5", - pos="e,2564.6,194.68 1864.4,251.9 1880.3,250 1896.9,248.25 1912.4,247 2145.6,228.26 2207.5,266.67 2438.4,229 2478.3,222.49 2522,209.29 \ -2554.8,198.08", + lp="2639.9,221.5", + pos="e,2557.2,194.17 2672.3,262.73 2613.5,259.22 2552.1,250.31 2533.4,229 2523,217.1 2532.7,206.69 2548.1,198.49", style=solid]; timepoint [color=blue, height=0.5, @@ -169,9 +167,8 @@ digraph { width=1.5346]; "drug to gene association" -> timepoint [color=blue, label=timepoint, - lp="2782.4,221.5", - pos="e,2771.6,195.19 1863.7,251.83 1879.8,249.91 1896.6,248.17 1912.4,247 2001.6,240.36 2632.4,256.97 2717.4,229 2734.4,223.39 2751,212.2 \ -2763.8,201.83", + lp="2786.4,221.5", + pos="e,2765.6,194.47 2766.8,247.2 2760.6,242.2 2754.9,236.11 2751.4,229 2746.7,219.42 2751.1,209.79 2758.4,201.57", style=solid]; "original subject" [color=blue, height=0.5, @@ -180,9 +177,8 @@ digraph { width=1.0652]; "drug to gene association" -> "original subject" [color=blue, label="original subject", - lp="2910.4,221.5", - pos="e,2882.7,194.25 1863.7,251.8 1879.8,249.88 1896.6,248.15 1912.4,247 2013.1,239.63 2724.7,258.08 2821.4,229 2840.8,223.18 2860,211.19 \ -2874.6,200.41", + lp="2900.4,221.5", + pos="e,2876.4,192.24 2811,246.75 2820.1,236.6 2832.3,223.86 2844.4,214 2851.6,208.17 2859.8,202.54 2867.7,197.56", style=solid]; "original predicate" [color=blue, height=0.5, @@ -191,47 +187,167 @@ digraph { width=1.5887]; "drug to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="3054.9,221.5", - pos="e,3004.9,195.82 1863.3,251.81 1879.6,249.88 1896.5,248.14 1912.4,247 1971,242.79 2917,253.67 2970.4,229 2981.9,223.67 2991.7,213.71 \ -2999,204.08", + lp="3042.9,221.5", + pos="e,2999.2,195.85 2886.3,252.47 2909.9,247.29 2934.8,239.8 2956.4,229 2969.5,222.46 2982,212.32 2992.1,202.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3146.4,178", + pos="3128.4,178", width=1.0652]; "drug to gene association" -> "original object" [color=blue, label="original object", - lp="3186.9,221.5", - pos="e,3143.1,196.02 1863.3,251.78 1879.6,249.85 1896.5,248.12 1912.4,247 1945.9,244.63 3094.1,247.11 3122.4,229 3130.7,223.67 3136.2,\ -214.55 3139.9,205.55", + lp="3170.9,221.5", + pos="e,3125.4,196.17 2885.7,252.36 2900.6,250.51 2915.9,248.65 2930.4,247 2969.5,242.53 3074.6,252.13 3106.4,229 3114.1,223.4 3119.1,\ +214.52 3122.4,205.79", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3261.4,178", + width=2.1304]; + "drug to gene association" -> "subject category" [color=blue, + label="subject category", + lp="3301.9,221.5", + pos="e,3254.3,196.03 2883.5,252.11 2899.1,250.22 2915.2,248.42 2930.4,247 2963.2,243.92 3197.6,245.1 3226.4,229 3236.1,223.56 3243.7,\ +214.18 3249.4,204.99", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3432.4,178", + width=2.1304]; + "drug to gene association" -> "object category" [color=blue, + label="object category", + lp="3449.9,221.5", + pos="e,3415.9,195.81 2882.8,251.95 2898.6,250.05 2915,248.3 2930.4,247 2978.6,242.95 3319.8,245.19 3365.4,229 3381.2,223.4 3396.3,212.69 \ +3408.2,202.61", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3565.4,178", + width=1.0652]; + "drug to gene association" -> "subject closure" [color=blue, + label="subject closure", + lp="3583.9,221.5", + pos="e,3549.9,194.72 2882.1,251.9 2898.1,249.99 2914.7,248.23 2930.4,247 2994.4,241.95 3448.6,252.57 3508.4,229 3516.2,225.92 3530.4,\ +213.5 3542.6,201.81", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3661.4,178", + width=1.0652]; + "drug to gene association" -> "object closure" [color=blue, + label="object closure", + lp="3703.4,221.5", + pos="e,3659,196.41 2882,251.83 2898.1,249.92 2914.7,248.19 2930.4,247 2969.7,244.01 3607.8,251.25 3640.4,229 3648.2,223.68 3653.1,214.85 \ +3656.2,206.09", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3794.4,178", + width=2.1304]; + "drug to gene association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3861.9,221.5", + pos="e,3786.8,196.21 2881.7,251.83 2897.8,249.9 2914.6,248.17 2930.4,247 2976.2,243.6 3716.6,250.13 3757.4,229 3767.6,223.73 3775.7,214.24 \ +3781.7,204.94", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3983.4,178", + width=2.1304]; + "drug to gene association" -> "object category closure" [color=blue, + label="object category closure", + lp="4051.9,221.5", + pos="e,3978.1,196.13 2881.7,251.77 2897.8,249.86 2914.6,248.14 2930.4,247 2958.7,244.96 3928.8,243.22 3953.4,229 3962.5,223.74 3969.2,\ +214.51 3973.9,205.4", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4173.4,178", + width=1.0652]; + "drug to gene association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4223.4,221.5", + pos="e,4166.7,196.2 2881.3,251.78 2897.6,249.85 2914.5,248.12 2930.4,247 2963.9,244.63 4109.8,244.93 4139.4,229 4149.1,223.77 4156.6,\ +214.42 4162,205.21", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4332.4,178", + width=1.0652]; + "drug to gene association" -> "object namespace" [color=blue, + label="object namespace", + lp="4376.4,221.5", + pos="e,4325,195.76 2881.3,251.76 2897.6,249.83 2914.5,248.11 2930.4,247 2968.2,244.36 4261.6,246.29 4295.4,229 4305.7,223.7 4313.9,214.02 \ +4319.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4483.4,178", + width=1.0652]; + "drug to gene association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4536.4,221.5", + pos="e,4475.4,195.78 2881.3,251.74 2897.6,249.82 2914.5,248.1 2930.4,247 2972.4,244.1 4406.7,247.68 4444.4,229 4455.1,223.69 4463.8,213.87 \ +4470.2,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4654.4,178", + width=1.0652]; + "drug to gene association" -> "object label closure" [color=blue, + label="object label closure", + lp="4702.9,221.5", + pos="e,4646.1,195.8 2881.3,251.73 2897.6,249.8 2914.5,248.09 2930.4,247 2977.1,243.8 4572.3,249.49 4614.4,229 4625.3,223.71 4634.1,213.89 \ +4640.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4816.4,178", + width=2.347]; + "drug to gene association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4864.9,221.5", + pos="e,4807.8,196.3 2881,251.76 2897.3,249.82 2914.4,248.09 2930.4,247 2981.6,243.52 4730.3,251.44 4776.4,229 4787.1,223.79 4795.9,214.17 \ +4802.4,204.76", style=solid]; type [height=0.5, - pos="3234.4,178", + pos="4950.4,178", width=0.86659]; "drug to gene association" -> type [color=blue, label=type, - lp="3264.4,221.5", - pos="e,3243.4,195.57 1863.3,251.76 1879.6,249.83 1896.5,248.11 1912.4,247 1930.8,245.71 3229.4,242.15 3242.4,229 3248.5,222.79 3248.7,\ -213.89 3246.6,205.31", + lp="4964.4,221.5", + pos="e,4951.2,196.19 2881,251.75 2897.3,249.81 2914.4,248.08 2930.4,247 2958.2,245.12 4916.6,246.37 4938.4,229 4945.2,223.55 4948.6,214.93 \ +4950.2,206.37", style=solid]; category [height=0.5, - pos="3335.4,178", + pos="5051.4,178", width=1.4263]; "drug to gene association" -> category [color=blue, label=category, - lp="3337.9,221.5", - pos="e,3323.7,195.89 1863.3,251.76 1879.6,249.83 1896.5,248.11 1912.4,247 1950.4,244.35 3249.2,243.64 3284.4,229 3297.2,223.66 3308.6,\ -213.42 3317.3,203.59", + lp="5043.9,221.5", + pos="e,5035.8,195.26 2881,251.74 2897.3,249.8 2914.4,248.08 2930.4,247 2987.3,243.15 4930.3,247.22 4984.4,229 5000.6,223.54 5016.1,212.52 \ +5028.1,202.21", style=solid]; object [height=0.5, pos="1238.4,91", width=1.0832]; "drug to gene association" -> object [color=blue, label=object, - lp="3427.4,178", - pos="e,1277.4,92.482 1863.3,251.75 1879.6,249.82 1896.5,248.1 1912.4,247 1952.9,244.19 3337.7,248.37 3373.4,229 3401.7,213.64 3417.8,\ -183.12 3395.4,160 3357.5,120.86 1605.8,96.685 1287.7,92.613", + lp="5142.4,178", + pos="e,1277.5,91.926 2881,251.74 2897.3,249.8 2914.4,248.08 2930.4,247 2990,242.99 5024.5,252.5 5079.4,229 5110.5,215.69 5135.1,184.11 \ +5111.4,160 5041.1,88.423 1733.3,91.209 1287.8,91.91", style=solid]; subject -> object [label=relation, lp="1237.4,134.5", @@ -244,18 +360,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="1959.4,265", + pos="2977.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2090.4,265", + pos="3108.4,265", width=2.0762]; object -> relation [pos="e,1196.2,35.54 1225.9,73.889 1219,64.939 1210.2,53.617 1202.4,43.584", style=dotted]; "drug to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="2293.4,265", + pos="3311.4,265", width=3.0692]; } diff --git a/graphviz/drug_to_gene_association.svg b/graphviz/drug_to_gene_association.svg index 6b3fb44d22..3839ec8c48 100644 --- a/graphviz/drug_to_gene_association.svg +++ b/graphviz/drug_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + drug to gene association - -drug to gene association + +drug to gene association @@ -24,9 +24,9 @@ drug to gene association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ drug to gene association->drug to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ drug to gene association->id - - -id + + +id @@ -63,9 +63,9 @@ drug to gene association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ drug to gene association->name - - -name + + +name @@ -89,9 +89,9 @@ drug to gene association->description - - -description + + +description @@ -102,9 +102,9 @@ drug to gene association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ drug to gene association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ drug to gene association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ drug to gene association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ drug to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ drug to gene association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ drug to gene association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ drug to gene association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ drug to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ drug to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ drug to gene association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ drug to gene association->original subject - - -original subject + + +original subject @@ -258,104 +258,247 @@ drug to gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string drug to gene association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +drug to gene association->subject category + + +subject category + + + +object category + +ontology class + + + +drug to gene association->object category + + +object category + + + +subject closure + +string + + + +drug to gene association->subject closure + + +subject closure + + + +object closure + +string + + + +drug to gene association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +drug to gene association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +drug to gene association->object category closure + + +object category closure + + + +subject namespace + +string + + + +drug to gene association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +drug to gene association->object namespace + + +object namespace + + + +subject label closure + +string + + + +drug to gene association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +drug to gene association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +drug to gene association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + drug to gene association->type - - -type + + +type - + category - -category + +category - + drug to gene association->category - - -category + + +category - + object object - + drug to gene association->object - - -object + + +object - + subject->object relation - + relation relation - + subject->relation - + association_type - -string + +string - + association_category - -category type + +category type - + object->relation - + drug to gene association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/druggable_gene_to_disease_association.gv b/graphviz/druggable_gene_to_disease_association.gv index f4a8a37cda..df4e4e6c65 100644 --- a/graphviz/druggable_gene_to_disease_association.gv +++ b/graphviz/druggable_gene_to_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4301.6,283"]; + graph [bb="0,0,6021.6,283"]; node [label="\N"]; "druggable gene to disease association" [height=0.5, label="druggable gene to disease association", - pos="2533.8,265", + pos="3343.8,265", width=5.2176]; "gene to disease association" [height=0.5, pos="137.79,178", width=3.8274]; "druggable gene to disease association" -> "gene to disease association" [label=is_a, - lp="769.79,221.5", - pos="e,234.59,190.82 2346.5,263.41 2022.3,261.69 1335.4,255 755.79,229 546.15,219.6 493.74,215.39 284.79,196 271.84,194.8 258.27,193.41 \ -244.83,191.95"]; + lp="763.79,221.5", + pos="e,234.59,190.81 3157,262.87 2643.7,259.56 1218.8,248.79 749.79,229 542.79,220.27 491.08,215.24 284.79,196 271.84,194.79 258.27,193.4 \ +244.83,191.94"]; "entity to disease association mixin" [height=0.5, pos="464.79,178", width=4.7482]; "druggable gene to disease association" -> "entity to disease association mixin" [label=uses, - lp="983.29,221.5", - pos="e,571.83,192.07 2345.8,264.47 2051.4,264.15 1464,259.27 966.79,229 834.59,220.95 683.42,204.97 581.81,193.23"]; + lp="974.29,221.5", + pos="e,569.41,192.26 3156.4,263.35 2671.5,261.32 1384.2,253.7 957.79,229 827.84,221.47 679.29,205.38 579.51,193.47"]; "gene to entity association mixin" [height=0.5, pos="812.79,178", width=4.4232]; "druggable gene to disease association" -> "gene to entity association mixin" [label=uses, - lp="1126.3,221.5", - pos="e,884.73,194.06 2347.2,262.71 2017.4,259.89 1344.1,251.49 1109.8,229 1036.6,221.98 954.21,207.58 894.8,196.04"]; + lp="1125.3,221.5", + pos="e,883.86,194.12 3157.4,262.7 2657.2,259 1309.6,247.42 1108.8,229 1035.6,222.28 953.15,207.78 893.91,196.12"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "druggable gene to disease association" -> id [color=blue, label=id, - lp="1245.8,221.5", - pos="e,1057.8,190 2346.9,262.95 2041.2,260.55 1447.5,252.89 1238.8,229 1165.8,220.64 1147.6,215.65 1076.8,196 1073.7,195.14 1070.5,194.17 \ -1067.3,193.16", + lp="1242.8,221.5", + pos="e,1057.8,189.98 3157.1,262.91 2677,259.82 1423.4,249.84 1235.8,229 1164.1,221.03 1146.3,215.43 1076.8,196 1073.7,195.13 1070.5,194.17 \ +1067.3,193.15", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "druggable gene to disease association" -> iri [color=blue, label=iri, - lp="1362.8,221.5", - pos="e,1162.7,190.23 2348.3,262.11 2066,258.62 1541.5,249.55 1354.8,229 1277.4,220.48 1258.2,215.26 1182.8,196 1179.4,195.14 1175.9,194.18 \ -1172.4,193.17", + lp="1355.8,221.5", + pos="e,1162.7,190.19 3157.5,262.64 2695.9,259.01 1524.2,248.03 1347.8,229 1273.4,220.98 1255.2,214.78 1182.8,196 1179.4,195.12 1175.9,\ +194.16 1172.5,193.14", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "druggable gene to disease association" -> name [color=blue, label=name, - lp="1465.8,221.5", - pos="e,1287.2,191.4 2347.3,262.83 2083.4,260.34 1614.2,252.64 1445.8,229 1394.1,221.74 1336.3,206.17 1296.8,194.32", + lp="1462.8,221.5", + pos="e,1286.5,191.54 3156.9,263.04 2710.9,260.4 1609.1,251.64 1442.8,229 1392,222.09 1335.4,206.57 1296.5,194.64", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "druggable gene to disease association" -> description [color=blue, label=description, - lp="1588.3,221.5", - pos="e,1433.9,193.98 2346.2,263.76 2103.9,262.33 1695.6,255.84 1547.8,229 1511.7,222.45 1472.5,209.01 1443.3,197.71", + lp="1583.3,221.5", + pos="e,1432.6,194.15 3156.3,263.69 2727.2,262.5 1698.1,256.74 1542.8,229 1507.9,222.77 1470.2,209.41 1442.1,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "druggable gene to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1729.8,221.5", - pos="e,1573.7,192.76 2346.8,262.92 2135.5,260.53 1805.1,252.94 1682.8,229 1648,222.19 1610.3,208.16 1582.9,196.69", + lp="1727.8,221.5", + pos="e,1573.2,192.94 3156.5,263.52 2752.1,261.97 1822.3,255.55 1680.8,229 1646.5,222.57 1609.5,208.61 1582.6,197.07", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "druggable gene to disease association" -> negated [color=blue, label=negated, - lp="1876.8,221.5", - pos="e,1694.8,190.58 2346.1,264.21 2207.7,261.99 2015.1,253.94 1847.8,229 1797.7,221.54 1741.9,205.56 1704.4,193.67", + lp="1881.8,221.5", + pos="e,1694.6,190.56 3155.7,264.57 2812.8,264.78 2098.9,261.16 1852.8,229 1800.9,222.22 1743,205.88 1704.5,193.71", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "druggable gene to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2003.3,221.5", - pos="e,1841.2,193.52 2346.8,263.02 2236.4,259.81 2094.3,251.09 1969.8,229 1929.1,221.77 1884.2,208.12 1851.1,196.91", + lp="2020.3,221.5", + pos="e,1843.1,193.2 3155.7,264.67 2837.6,264.88 2206.4,261.05 1986.8,229 1940.7,222.28 1889.8,207.98 1853,196.39", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "druggable gene to disease association" -> publications [color=blue, label=publications, - lp="2130.8,221.5", - pos="e,1989.3,193.86 2349,261.71 2267.7,257.59 2171.7,248.45 2086.8,229 2056.3,222.01 2023.5,209.07 1998.7,198.1", + lp="2163.8,221.5", + pos="e,1993.9,192.96 3156,264.87 2863.6,265.16 2313.2,261.18 2119.8,229 2079.5,222.3 2035.3,208.04 2003.4,196.46", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=3.015]; "druggable gene to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2264.3,221.5", - pos="e,2160.3,195.94 2367.3,256.57 2299.5,251.48 2229.9,243.01 2199.8,229 2187.4,223.23 2176.1,213.26 2167.2,203.74", + lp="2317.3,221.5", + pos="e,2174.7,195.64 3158.2,262.19 2869.8,258.75 2338,249.68 2252.8,229 2228.6,223.12 2203.3,211.28 2183.6,200.6", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=3.015]; "druggable gene to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2430.8,221.5", - pos="e,2351.6,195.46 2396.5,252.67 2368.6,247.5 2345,239.97 2335.8,229 2328,219.76 2333.8,210.01 2343.5,201.6", + lp="2489.8,221.5", + pos="e,2382,196.1 3157.1,262.86 2889,260.39 2423.7,252.7 2394.8,229 2388,223.45 2384.7,214.81 2383.1,206.27", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "druggable gene to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2641.3,221.5", - pos="e,2559.7,193.23 2529.7,246.85 2528.3,236.48 2528.4,223.49 2534.8,214 2539,207.77 2544.6,202.65 2550.8,198.43", + lp="2699.3,221.5", + pos="e,2600,195.83 3159.1,261.7 2943.1,258.08 2612.1,249.26 2592.8,229 2586,221.87 2588.5,212.53 2594,203.85", style=solid]; timepoint [color=blue, height=0.5, @@ -143,8 +143,8 @@ digraph { width=1.5346]; "druggable gene to disease association" -> timepoint [color=blue, label=timepoint, - lp="2803.8,221.5", - pos="e,2787.1,195.66 2675.7,253.15 2700.6,247.83 2725.6,240.12 2747.8,229 2760,222.87 2771.3,212.85 2780.2,203.39", + lp="2855.8,221.5", + pos="e,2802.3,196.26 3160.2,261.08 3020.7,257.31 2848.4,248.68 2820.8,229 2813.1,223.52 2808.2,214.66 2805.1,205.91", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,8 +153,8 @@ digraph { width=1.0652]; "druggable gene to disease association" -> "original subject" [color=blue, label="original subject", - lp="2918.8,221.5", - pos="e,2891.6,193.57 2665.1,252.08 2740.7,244.68 2824,235.39 2840.8,229 2843.3,228.05 2864.7,212.91 2883.3,199.53", + lp="2954.8,221.5", + pos="e,2900.7,195.28 3160.1,261.1 3045.8,257.33 2917,248.7 2898.8,229 2892.6,222.33 2893.4,213.1 2896.5,204.39", style=solid]; "original predicate" [color=blue, height=0.5, @@ -163,9 +163,8 @@ digraph { width=1.5887]; "druggable gene to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3060.3,221.5", - pos="e,3013.9,196.09 2667,252.27 2688.3,250.46 2710.2,248.65 2730.8,247 2785.2,242.65 2926.2,251.73 2975.8,229 2988,223.41 2998.9,213.47 \ -3007.4,203.92", + lp="3083.3,221.5", + pos="e,3017.8,195.83 3181.3,255.92 3106.4,250.5 3031.4,241.92 3019.8,229 3014.1,222.71 3013.6,214.04 3015.1,205.68", style=solid]; "original object" [color=blue, height=0.5, @@ -174,135 +173,251 @@ digraph { width=1.0652]; "druggable gene to disease association" -> "original object" [color=blue, label="original object", - lp="3188.3,221.5", - pos="e,3139.8,196.14 2664.1,252.01 2686.3,250.17 2709.2,248.42 2730.8,247 2752.7,245.56 3108.6,242.67 3125.8,229 3132.8,223.44 3136.5,\ -214.68 3138.3,206.04", + lp="3214.3,221.5", + pos="e,3143.5,196.37 3230.9,250.59 3201.3,245.24 3174.4,238.14 3162.8,229 3155.4,223.23 3150.4,214.58 3146.9,206.09", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3272.8,178", + width=2.1304]; + "druggable gene to disease association" -> "subject category" [color=blue, + label="subject category", + lp="3333.3,221.5", + pos="e,3269,196.01 3293.6,247.52 3285.8,242.76 3278.7,236.7 3273.8,229 3269.5,222.26 3268.2,213.93 3268.2,206.01", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3443.8,178", + width=2.1304]; + "druggable gene to disease association" -> "object category" [color=blue, + label="object category", + lp="3465.3,221.5", + pos="e,3427.9,195.89 3369,247.1 3376.8,241.57 3385.3,235.25 3392.8,229 3402.3,220.99 3412.3,211.56 3420.8,203.06", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3576.8,178", + width=1.0652]; + "druggable gene to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3600.3,221.5", + pos="e,3564.4,195.04 3463,251.08 3484.3,245.97 3505.8,238.87 3524.8,229 3537.2,222.54 3548.8,212.16 3557.8,202.52", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3676.8,178", + width=1.0652]; + "druggable gene to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3719.8,221.5", + pos="e,3675.2,196.05 3477.7,252.34 3560.1,244.63 3651.3,234.89 3658.8,229 3666,223.33 3670.3,214.55 3672.9,205.92", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3809.8,178", + width=2.1304]; + "druggable gene to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3878.3,221.5", + pos="e,3802.4,195.98 3477.3,252.32 3498.5,250.5 3520.3,248.68 3540.8,247 3592.5,242.77 3728.5,254.44 3773.8,229 3783.6,223.5 3791.4,214.1 \ +3797.2,204.92", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4001.8,178", + width=2.1304]; + "druggable gene to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4069.3,221.5", + pos="e,3995.7,196.07 3473.5,251.98 3496,250.14 3519,248.39 3540.8,247 3588.4,243.95 3928.4,252.78 3969.8,229 3979.2,223.61 3986.2,214.23 \ +3991.3,205.04", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4191.8,178", + width=1.0652]; + "druggable gene to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4241.8,221.5", + pos="e,4184.8,196.16 3472.2,251.86 3495,250 3518.6,248.28 3540.8,247 3575,245.03 4126.7,245.25 4156.8,229 4166.6,223.72 4174.2,214.36 \ +4179.8,205.15", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4350.8,178", + width=1.0652]; + "druggable gene to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4394.8,221.5", + pos="e,4343.4,195.71 3471.7,251.79 3494.7,249.93 3518.4,248.22 3540.8,247 3583.7,244.65 4275.7,248.78 4313.8,229 4324.1,223.65 4332.3,\ +213.96 4338.3,204.53", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4501.8,178", + width=1.0652]; + "druggable gene to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4554.8,221.5", + pos="e,4493.8,195.75 3471.1,251.76 3494.3,249.89 3518.2,248.19 3540.8,247 3591.9,244.3 4417,251.93 4462.8,229 4473.5,223.64 4482.1,213.82 \ +4488.5,204.29", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4672.8,178", + width=1.0652]; + "druggable gene to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4720.3,221.5", + pos="e,4664.5,195.78 3470.9,251.73 3494.1,249.85 3518.2,248.16 3540.8,247 3571.1,245.44 4605.6,242.37 4632.8,229 4643.6,223.67 4652.5,\ +213.86 4659.1,204.32", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4813.8,178", + width=2.347]; + "druggable gene to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4875.3,221.5", + pos="e,4811.7,196.42 3470.6,251.71 3493.9,249.83 3518.1,248.14 3540.8,247 3575.6,245.25 4765.1,248.72 4793.8,229 4801.5,223.69 4806.3,\ +214.87 4809.2,206.1", style=solid]; type [height=0.5, - pos="3227.8,178", + pos="4947.8,178", width=0.86659]; "druggable gene to disease association" -> type [color=blue, label=type, - lp="3264.8,221.5", - pos="e,3240.1,194.84 2663,251.9 2685.6,250.06 2708.9,248.33 2730.8,247 2759.3,245.27 3224,249.52 3243.8,229 3250.4,222.19 3249,212.67 \ -3245,203.76", + lp="4971.8,221.5", + pos="e,4953.7,196.12 3470.6,251.68 3493.9,249.8 3518.1,248.12 3540.8,247 3560.3,246.03 4935,242.92 4948.8,229 4954.7,223.03 4956,214.43 \ +4955.3,206.05", style=solid]; category [height=0.5, - pos="3328.8,178", + pos="5048.8,178", width=1.4263]; "druggable gene to disease association" -> category [color=blue, label=category, - lp="3335.3,221.5", - pos="e,3319.2,195.75 2662.7,251.87 2685.4,250.03 2708.8,248.31 2730.8,247 2792.3,243.35 3229.1,255.28 3284.8,229 3296.3,223.58 3306,213.61 \ -3313.4,203.99", + lp="5048.3,221.5", + pos="e,5035.8,195.44 3470.3,251.69 3493.7,249.81 3518,248.12 3540.8,247 3581,245.02 4954.2,243.43 4991.8,229 5005.9,223.59 5018.8,212.98 \ +5028.8,202.93", style=solid]; object [height=0.5, - pos="3899.8,91", + pos="5619.8,91", width=1.0832]; "druggable gene to disease association" -> object [color=blue, label=object, - lp="3446.8,178", - pos="e,3861,93.851 2662.2,251.84 2685,249.98 2708.6,248.27 2730.8,247 2766.3,244.97 3339,245.03 3370.8,229 3405.6,211.45 3391.1,179.5 \ -3424.8,160 3496.7,118.42 3744.7,100.36 3850.9,94.406", + lp="5166.8,178", + pos="e,5581.1,94.108 3470.3,251.68 3493.7,249.8 3518,248.12 3540.8,247 3583.6,244.91 5044.8,246.84 5083.8,229 5121,211.96 5108.8,179.43 \ +5144.8,160 5217.9,120.59 5465.2,101.32 5571.1,94.725", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3562.8,178", + pos="5282.8,178", width=2.3651]; "druggable gene to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3550.8,221.5", - pos="e,3530.3,194.7 2661.9,251.81 2684.8,249.96 2708.5,248.25 2730.8,247 2885.9,238.32 3277.3,258.75 3429.8,229 3461.3,222.84 3495.2,\ -209.99 3520.9,198.86", + lp="5270.8,221.5", + pos="e,5250.6,194.72 3470.3,251.67 3493.7,249.79 3518,248.11 3540.8,247 3630.1,242.65 5061.9,245.48 5149.8,229 5181.5,223.05 5215.5,210.13 \ +5241.2,198.91", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="3741.8,178", + pos="5461.8,178", width=2.1123]; "druggable gene to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="3731.8,221.5", - pos="e,3713,194.76 2661.4,251.75 2684.5,249.89 2708.3,248.19 2730.8,247 2829.8,241.74 3525.8,249.57 3622.8,229 3651.1,222.99 3681.2,210.31 \ -3704,199.23", + lp="5451.8,221.5", + pos="e,5433,194.85 3470.1,251.67 3493.6,249.78 3517.9,248.1 3540.8,247 3640.8,242.19 5244.7,249.27 5342.8,229 5371.1,223.14 5401.2,210.46 \ +5424,199.33", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="3871.8,178", + pos="5591.8,178", width=1.011]; "druggable gene to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="3880.3,221.5", - pos="e,3855.1,194.26 2660.9,251.73 2684.1,249.86 2708.2,248.17 2730.8,247 2789.9,243.95 3740.2,246.64 3796.8,229 3815.2,223.25 3833.3,\ -211.43 3847.1,200.72", + lp="5600.3,221.5", + pos="e,5575.1,194.31 3470.1,251.65 3493.6,249.77 3517.9,248.09 3540.8,247 3595.6,244.39 5464.3,245.15 5516.8,229 5535.2,223.32 5553.3,\ +211.5 5567.1,200.78", style=solid]; subject [height=0.5, - pos="3970.8,178", + pos="5690.8,178", width=1.2277]; "druggable gene to disease association" -> subject [color=blue, label=subject, - lp="3978.8,221.5", - pos="e,3963.8,196.21 2660.6,251.72 2683.9,249.84 2708.1,248.15 2730.8,247 2764.2,245.31 3906.2,244.68 3935.8,229 3945.6,223.79 3953.3,\ -214.44 3958.9,205.23", + lp="5698.8,221.5", + pos="e,5683.8,196.24 3470.1,251.64 3493.6,249.76 3517.9,248.08 3540.8,247 3570.1,245.61 5629.8,242.68 5655.8,229 5665.6,223.82 5673.3,\ +214.48 5678.9,205.26", style=solid]; predicate [height=0.5, - pos="4087.8,178", + pos="5807.8,178", width=1.5165]; "druggable gene to disease association" -> predicate [color=blue, label=predicate, - lp="4075.8,221.5", - pos="e,4069.1,195.02 2660.6,251.7 2683.9,249.83 2708.1,248.14 2730.8,247 2801.7,243.45 3940.7,249.25 4008.8,229 4027.8,223.35 4046.6,\ -211.72 4061.1,201.1", + lp="5795.8,221.5", + pos="e,5789.2,195.06 3470.1,251.64 3493.6,249.75 3517.9,248.08 3540.8,247 3601.5,244.14 5670.5,246.16 5728.8,229 5747.8,223.41 5766.6,\ +211.78 5781.1,201.15", style=solid]; "has evidence" [height=0.5, - pos="4230.8,178", + pos="5950.8,178", width=1.9679]; "druggable gene to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="4206.3,221.5", - pos="e,4203,194.58 2660.6,251.68 2683.9,249.81 2708.1,248.13 2730.8,247 2807.5,243.19 4038.6,244.9 4113.8,229 4141.8,223.08 4171.4,210.36 \ -4193.8,199.22", + lp="5926.3,221.5", + pos="e,5923,194.62 3469.8,251.65 3493.4,249.76 3517.8,248.08 3540.8,247 3668,241.02 5709.1,255.04 5833.8,229 5861.8,223.15 5891.4,210.43 \ +5913.8,199.28", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2777.8,265", + pos="3587.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2908.8,265", + pos="3718.8,265", width=2.0762]; relation [height=0.5, - pos="3934.8,18", + pos="5654.8,18", width=1.2999]; - object -> relation [pos="e,3926.3,36.198 3908.1,73.174 3912.2,64.896 3917.2,54.723 3921.8,45.438", + object -> relation [pos="e,5646.3,36.198 5628.1,73.174 5632.2,64.896 5637.2,54.723 5641.8,45.438", style=dotted]; "gene to disease association_object" [color=blue, height=0.5, label=disease, - pos="3046.8,265", + pos="3856.8,265", width=1.2638]; subject -> object [label=relation, - lp="3928.8,134.5", - pos="e,3896,109.01 3934.4,167.42 3921.6,162.12 3908.4,154.06 3900.8,142 3896.5,135.26 3895.2,126.93 3895.2,119.01"]; - subject -> relation [pos="e,3939,36.005 3967.1,160.05 3962.7,139.44 3954.9,103.63 3947.8,73 3945.8,64.183 3943.5,54.574 3941.4,45.938", + lp="5648.8,134.5", + pos="e,5616,109.01 5654.4,167.42 5641.6,162.12 5628.4,154.06 5620.8,142 5616.5,135.26 5615.2,126.93 5615.2,119.01"]; + subject -> relation [pos="e,5659,36.005 5687.1,160.05 5682.7,139.44 5674.9,103.63 5667.8,73 5665.8,64.183 5663.5,54.574 5661.4,45.938", style=dotted]; "druggable gene to disease association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3220.8,265", + pos="4030.8,265", width=3.0692]; "druggable gene to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3426.8,265", + pos="4236.8,265", width=2.1665]; "druggable gene to disease association_has evidence" [color=blue, height=0.5, label=DruggableGeneCategoryEnum, - pos="3675.8,265", + pos="4485.8,265", width=4.2607]; } diff --git a/graphviz/druggable_gene_to_disease_association.svg b/graphviz/druggable_gene_to_disease_association.svg index f24bdca2f4..3a4510f5c0 100644 --- a/graphviz/druggable_gene_to_disease_association.svg +++ b/graphviz/druggable_gene_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + druggable gene to disease association - -druggable gene to disease association + +druggable gene to disease association @@ -24,9 +24,9 @@ druggable gene to disease association->gene to disease association - - -is_a + + +is_a @@ -37,9 +37,9 @@ druggable gene to disease association->entity to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ druggable gene to disease association->gene to entity association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ druggable gene to disease association->id - - -id + + +id @@ -76,9 +76,9 @@ druggable gene to disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ druggable gene to disease association->name - - -name + + +name @@ -102,9 +102,9 @@ druggable gene to disease association->description - - -description + + +description @@ -115,9 +115,9 @@ druggable gene to disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ druggable gene to disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ druggable gene to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ druggable gene to disease association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ druggable gene to disease association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ druggable gene to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ druggable gene to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ druggable gene to disease association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ druggable gene to disease association->original subject - - -original subject + + +original subject @@ -232,9 +232,9 @@ druggable gene to disease association->original predicate - - -original predicate + + +original predicate @@ -245,187 +245,330 @@ druggable gene to disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +druggable gene to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +druggable gene to disease association->object category + + +object category + + + +subject closure + +string + + + +druggable gene to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +druggable gene to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +druggable gene to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +druggable gene to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +druggable gene to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +druggable gene to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +druggable gene to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +druggable gene to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +druggable gene to disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + druggable gene to disease association->type - - -type + + +type - + category - -category + +category - + druggable gene to disease association->category - - -category + + +category - + object - -object + +object - + druggable gene to disease association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + druggable gene to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + druggable gene to disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + druggable gene to disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + subject - -subject + +subject - + druggable gene to disease association->subject - - -subject + + +subject - + predicate - -predicate + +predicate - + druggable gene to disease association->predicate - - -predicate + + +predicate - + has evidence - -has evidence + +has evidence - + druggable gene to disease association->has evidence - - -has evidence + + +has evidence - + association_type - -string + +string - + association_category - -category type + +category type - + relation - -relation + +relation - + object->relation - - + + - + gene to disease association_object - -disease + +disease - + subject->object - - -relation + + +relation - + subject->relation - - + + - + druggable gene to disease association_subject - -gene or gene product + +gene or gene product - + druggable gene to disease association_predicate - -predicate type + +predicate type - + druggable gene to disease association_has evidence - -DruggableGeneCategoryEnum + +DruggableGeneCategoryEnum diff --git a/graphviz/entity_to_disease_association.gv b/graphviz/entity_to_disease_association.gv index 284ae40af5..86ee270b4d 100644 --- a/graphviz/entity_to_disease_association.gv +++ b/graphviz/entity_to_disease_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3446.4,283"]; + graph [bb="0,0,5142.4,283"]; node [label="\N"]; "entity to disease association" [height=0.5, label="entity to disease association", - pos="1523.4,265", + pos="2544.4,265", width=3.9538]; association [height=0.5, pos="62.394,178", width=1.7332]; "entity to disease association" -> association [label=is_a, lp="280.39,221.5", - pos="e,103.32,191.76 1381.1,263.84 1099,262.89 477.81,257.52 266.39,229 213.31,221.84 153.98,206.43 113.05,194.6"]; + pos="e,102.91,191.8 2402.4,263.68 1937.3,262.36 477.01,256.08 266.39,229 213.1,222.15 153.57,206.62 112.64,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "entity to disease association" -> id [color=blue, label=id, - lp="397.39,221.5", - pos="e,210.38,189.99 1382.1,262.66 1122.2,259.68 578.16,250.98 390.39,229 317.85,220.51 299.77,215.57 229.39,196 226.29,195.14 223.09,\ -194.17 219.89,193.15", + lp="396.39,221.5", + pos="e,210.38,189.98 2402.7,263.24 1955,260.62 587.97,250.9 389.39,229 317.22,221.04 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "entity to disease association" -> iri [color=blue, label=iri, - lp="513.39,221.5", - pos="e,315.3,190.22 1382.9,261.9 1144.7,257.89 671,247.8 505.39,229 428.92,220.32 409.95,215.12 335.39,196 332.02,195.13 328.54,194.17 \ -325.05,193.16", + lp="503.39,221.5", + pos="e,315.31,190.16 2402.5,263.11 1969.5,260.17 683.15,249.78 495.39,229 423.23,221.01 405.62,214.45 335.39,196 332.02,195.11 328.55,\ +194.14 325.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "entity to disease association" -> name [color=blue, label=name, - lp="615.39,221.5", - pos="e,439.55,191.43 1382.4,262.38 1161.3,259.22 742.86,250.53 595.39,229 544.85,221.62 488.44,206.25 449.54,194.49", + lp="607.39,221.5", + pos="e,438.25,191.78 2402.6,263.47 1982.9,261.61 765.15,254.09 587.39,229 538.92,222.16 485.05,206.79 447.81,194.88", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "entity to disease association" -> description [color=blue, label=description, - lp="729.89,221.5", - pos="e,584.6,194.29 1381.6,263.26 1179.2,261.32 817.62,254.3 689.39,229 656.44,222.5 620.84,209.44 594.05,198.29", + lp="723.89,221.5", + pos="e,582.77,194.4 2401.9,264.13 1995.6,264.09 849.98,261.11 683.39,229 651.71,222.89 617.7,209.84 592.13,198.6", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "entity to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="866.39,221.5", - pos="e,723.86,193.3 1382.3,262.57 1208.3,259.83 922.82,251.9 819.39,229 789.19,222.31 756.86,208.9 732.93,197.65", + lp="862.39,221.5", + pos="e,722.86,193.55 2402,264.19 2016,264.26 968.26,261.42 815.39,229 786.11,222.79 754.98,209.44 731.91,198.1", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { "entity to disease association" -> subject [color=blue, label=subject, lp="989.39,221.5", - pos="e,867.11,194.24 1385.7,260.31 1246.4,255.69 1040.8,246.21 963.39,229 933.27,222.3 900.94,209.48 876.43,198.5", + pos="e,866.52,194.37 2402.2,263.71 2040.1,262.55 1101.9,256.88 963.39,229 932.94,222.87 900.37,209.91 875.84,198.72", style=solid]; predicate [color=blue, height=0.5, @@ -81,7 +81,7 @@ digraph { "entity to disease association" -> predicate [color=blue, label=predicate, lp="1068.4,221.5", - pos="e,1008.5,195.95 1385.7,260.42 1251.7,255.94 1064,246.6 1034.4,229 1025.2,223.53 1018.2,214.26 1013.1,205.18", + pos="e,1008.4,196.14 2402.2,264.3 2037.4,264.6 1093.3,262.14 1034.4,229 1025,223.7 1017.9,214.33 1012.8,205.13", style=solid]; object [color=blue, height=0.5, @@ -91,8 +91,8 @@ digraph { "entity to disease association" -> object [color=blue, label=object, lp="1147.4,178", - pos="e,976.03,105.47 1440.7,250.29 1402.3,243.89 1356,236.12 1314.4,229 1230.3,214.62 1201.1,235.31 1125.4,196 1105.3,185.57 1108.1,172.77 \ -1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", + pos="e,976.03,105.47 2403.8,262.06 2132.3,257.95 1544.4,247.23 1342.4,229 1245.2,220.23 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,\ +172.77 1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", style=solid]; negated [color=blue, height=0.5, @@ -101,8 +101,8 @@ digraph { width=1.2999]; "entity to disease association" -> negated [color=blue, label=negated, - lp="1393.4,221.5", - pos="e,1256.5,191.48 1448.5,249.58 1421.8,243.89 1391.6,236.84 1364.4,229 1330.8,219.31 1293.6,205.77 1266.1,195.22", + lp="1452.4,221.5", + pos="e,1260,190.39 2402.7,263.03 2144.9,260.69 1608.5,253.01 1423.4,229 1369.6,222.02 1309.4,205.52 1269.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -111,8 +111,8 @@ digraph { width=2.1304]; "entity to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1485.9,221.5", - pos="e,1392.9,195.02 1488.5,247.38 1476.9,241.72 1464,235.24 1452.4,229 1435.5,219.92 1417,209.3 1401.6,200.19", + lp="1585.9,221.5", + pos="e,1408.3,193.2 2402.7,262.96 2168.8,260.58 1712,252.94 1552.4,229 1506.1,222.05 1454.8,207.75 1417.8,196.22", style=solid]; publications [color=blue, height=0.5, @@ -121,8 +121,8 @@ digraph { width=1.7332]; "entity to disease association" -> publications [color=blue, label=publications, - lp="1567.4,221.5", - pos="e,1523.4,196.18 1523.4,246.8 1523.4,235.16 1523.4,219.55 1523.4,206.24", + lp="1724.4,221.5", + pos="e,1558.3,193.08 2402.8,262.85 2194.3,260.38 1814.8,252.69 1680.4,229 1641.5,222.15 1598.9,208.14 1567.9,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -131,8 +131,8 @@ digraph { width=2.0943]; "entity to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="1684.9,221.5", - pos="e,1661.1,195.69 1573.3,248.11 1587.3,242.83 1602.3,236.39 1615.4,229 1628.7,221.48 1642.3,211.34 1653.5,202.15", + lp="1871.9,221.5", + pos="e,1714.3,194.09 2404,261.84 2226.8,258.3 1932.3,249.49 1825.4,229 1790.4,222.3 1752.4,209.09 1724,197.93", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -141,8 +141,8 @@ digraph { width=3.015]; "entity to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1848.9,221.5", - pos="e,1841.3,194.73 1619.1,251.66 1655.7,246.03 1697.8,238.48 1735.4,229 1768,220.77 1803.8,208.57 1831.8,198.28", + lp="2011.9,221.5", + pos="e,1897.9,195.96 2407.3,260.16 2244.4,254.94 1989.3,244.45 1947.4,229 1931.9,223.3 1917.1,212.69 1905.4,202.7", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -151,9 +151,8 @@ digraph { width=3.015]; "entity to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2084.4,221.5", - pos="e,2066.6,194.05 1623.9,252.23 1641.1,250.37 1658.7,248.55 1675.4,247 1782.8,237 1810.9,246.2 1917.4,229 1964.9,221.33 2017.7,207.83 \ -2056.9,196.8", + lp="2178.4,221.5", + pos="e,2094.1,195.74 2402.9,262.76 2275.5,260.13 2104.9,252.25 2083.4,229 2076.2,221.21 2080,211.68 2087.1,203.04", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -162,9 +161,8 @@ digraph { width=3.015]; "entity to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2351.9,221.5", - pos="e,2309.6,194.66 1621.4,251.93 1639.3,250.04 1657.9,248.29 1675.4,247 1900.7,230.43 1960.4,265.52 2183.4,229 2223.3,222.47 2267,209.26 \ -2299.8,198.06", + lp="2387.9,221.5", + pos="e,2304.5,194.27 2404.5,261.66 2350.9,257.53 2298.4,248.41 2281.4,229 2271.3,217.45 2280.6,207.11 2295.3,198.87", style=solid]; timepoint [color=blue, height=0.5, @@ -173,9 +171,8 @@ digraph { width=1.5346]; "entity to disease association" -> timepoint [color=blue, label=timepoint, - lp="2527.4,221.5", - pos="e,2516.6,195.19 1620.6,251.84 1638.8,249.93 1657.6,248.19 1675.4,247 1762.7,241.13 2379.3,256.37 2462.4,229 2479.4,223.39 2496,212.2 \ -2508.8,201.82", + lp="2534.4,221.5", + pos="e,2512,194.95 2514.8,247.2 2508.6,242.2 2502.9,236.11 2499.4,229 2494.9,219.85 2498.7,210.46 2505.2,202.32", style=solid]; "original subject" [color=blue, height=0.5, @@ -184,9 +181,8 @@ digraph { width=1.0652]; "entity to disease association" -> "original subject" [color=blue, label="original subject", - lp="2655.4,221.5", - pos="e,2627.7,194.25 1620.6,251.8 1638.8,249.89 1657.6,248.17 1675.4,247 1774.2,240.49 2471.6,257.53 2566.4,229 2585.8,223.18 2605,211.18 \ -2619.6,200.4", + lp="2648.4,221.5", + pos="e,2622.4,192.59 2559.1,246.86 2568.2,236.75 2580.4,224.01 2592.4,214 2599.1,208.42 2606.7,202.95 2614,198.05", style=solid]; "original predicate" [color=blue, height=0.5, @@ -195,49 +191,168 @@ digraph { width=1.5887]; "entity to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="2799.9,221.5", - pos="e,2749.9,195.81 1620.2,251.8 1638.5,249.88 1657.5,248.15 1675.4,247 1733.1,243.28 2662.9,253.26 2715.4,229 2726.9,223.67 2736.7,\ -213.71 2744,204.07", + lp="2789.9,221.5", + pos="e,2745.2,195.87 2639.9,251.62 2661.8,246.49 2684.6,239.24 2704.4,229 2716.9,222.55 2728.7,212.55 2738.2,203.17", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2909.4,178", + pos="2873.4,178", width=1.0652]; "entity to disease association" -> "original object" [color=blue, label="original object", - lp="2938.9,221.5", - pos="e,2900.5,195.8 1620.2,251.76 1638.5,249.85 1657.5,248.13 1675.4,247 1708.4,244.91 2837.5,243.21 2867.4,229 2878.5,223.71 2887.8,\ -213.9 2894.7,204.35", + lp="2917.9,221.5", + pos="e,2871.5,196.07 2647.1,252.49 2737.2,242.36 2854.1,229.2 2854.4,229 2861.7,223.35 2866.2,214.58 2868.9,205.94", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3006.4,178", + width=2.1304]; + "entity to disease association" -> "subject category" [color=blue, + label="subject category", + lp="3048.9,221.5", + pos="e,3000,195.99 2644.5,252.14 2661.8,250.28 2679.6,248.48 2696.4,247 2727.1,244.29 2946.7,244.49 2973.4,229 2982.8,223.52 2990.1,214.12 \ +2995.4,204.94", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3177.4,178", + width=2.1304]; + "entity to disease association" -> "object category" [color=blue, + label="object category", + lp="3195.9,221.5", + pos="e,3161.5,195.8 2643.2,251.96 2660.9,250.09 2679.2,248.33 2696.4,247 2742.5,243.43 3068.9,244.84 3112.4,229 3127.8,223.38 3142.6,\ +212.67 3154.1,202.6", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3310.4,178", + width=1.0652]; + "entity to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3333.9,221.5", + pos="e,3297.9,195.33 2642.4,251.88 2660.3,250 2678.9,248.26 2696.4,247 2758.4,242.54 3197.8,252.34 3255.4,229 3269.1,223.44 3281.6,212.82 \ +3291.2,202.79", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3408.4,178", + width=1.0652]; + "entity to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3450.4,221.5", + pos="e,3406.3,196.38 2642,251.84 2660.1,249.94 2678.8,248.21 2696.4,247 2734.8,244.36 3356.8,250.97 3388.4,229 3396.1,223.64 3400.8,214.81 \ +3403.7,206.05", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3541.4,178", + width=2.1304]; + "entity to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3608.9,221.5", + pos="e,3533.8,196.21 2641.6,251.83 2659.8,249.92 2678.6,248.19 2696.4,247 2741.2,244 3464.5,249.65 3504.4,229 3514.6,223.73 3522.7,214.24 \ +3528.7,204.93", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3731.4,178", + width=2.1304]; + "entity to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="3798.9,221.5", + pos="e,3725.7,196.14 2641.6,251.76 2659.8,249.86 2678.6,248.15 2696.4,247 2724.2,245.2 3676.1,242.78 3700.4,229 3709.6,223.76 3716.5,\ +214.53 3721.3,205.42", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3921.4,178", + width=1.0652]; + "entity to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3971.4,221.5", + pos="e,3914.7,195.72 2641.2,251.77 2659.5,249.85 2678.5,248.13 2696.4,247 2729.4,244.91 3857.2,244.49 3886.4,229 3896.5,223.66 3904.3,\ +213.97 3909.9,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4080.4,178", + width=1.0652]; + "entity to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4124.4,221.5", + pos="e,4073,195.75 2641.2,251.74 2659.5,249.83 2678.5,248.12 2696.4,247 2733.7,244.67 4010.1,246.07 4043.4,229 4053.7,223.7 4061.9,214.02 \ +4067.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4231.4,178", + width=1.0652]; + "entity to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4284.4,221.5", + pos="e,4223.4,195.78 2641.2,251.72 2659.5,249.81 2678.5,248.11 2696.4,247 2737.9,244.44 4155.2,247.46 4192.4,229 4203.1,223.68 4211.8,\ +213.87 4218.2,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4402.4,178", + width=1.0652]; + "entity to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4450.9,221.5", + pos="e,4394.1,195.8 2640.8,251.74 2659.2,249.82 2678.4,248.1 2696.4,247 2742.6,244.17 4320.8,249.27 4362.4,229 4373.3,223.71 4382.1,213.89 \ +4388.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4564.4,178", + width=2.347]; + "entity to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4612.9,221.5", + pos="e,4555.8,196.3 2640.8,251.73 2659.2,249.81 2678.4,248.09 2696.4,247 2747.1,243.92 4478.7,251.22 4524.4,229 4535.1,223.79 4543.9,\ +214.17 4550.4,204.76", style=solid]; type [height=0.5, - pos="3016.4,178", + pos="4712.4,178", width=0.86659]; "entity to disease association" -> type [color=blue, label=type, - lp="3023.4,221.5", - pos="e,3013.8,195.98 1620.2,251.74 1638.5,249.83 1657.5,248.12 1675.4,247 1712,244.71 2963.8,249.23 2994.4,229 3002.4,223.67 3007.6,214.69 \ -3010.8,205.79", + lp="4716.4,221.5", + pos="e,4708.4,196.08 2640.8,251.72 2659.2,249.8 2678.4,248.09 2696.4,247 2724,245.34 4662.8,243.45 4686.4,229 4695,223.74 4700.9,214.64 \ +4704.8,205.63", style=solid]; category [height=0.5, - pos="3117.4,178", + pos="4813.4,178", width=1.4263]; "entity to disease association" -> category [color=blue, label=category, - lp="3105.9,221.5", - pos="e,3100.1,195.01 1620.2,251.74 1638.5,249.82 1657.5,248.12 1675.4,247 1751.3,242.27 2970.9,251.73 3043.4,229 3061.3,223.39 3078.8,\ -211.93 3092.3,201.39", + lp="4799.9,221.5", + pos="e,4795.3,195.05 2640.8,251.72 2659.2,249.79 2678.4,248.08 2696.4,247 2753,243.6 4682.1,245.33 4736.4,229 4754.8,223.45 4773,211.98 \ +4787.1,201.44", style=solid]; "FDA approval status" [color=blue, height=0.5, label=FDAApprovalStatusEnum, - pos="3316.4,178", + pos="5012.4,178", width=3.6108]; "entity to disease association" -> "FDA approval status" [color=blue, label="FDA approval status", - lp="3283.9,221.5", - pos="e,3272.5,195.06 1620.2,251.72 1638.5,249.81 1657.5,248.11 1675.4,247 1838,236.93 2980.2,252.58 3141.4,229 3182.9,222.92 3228.5,209.68 \ -3262.7,198.35", + lp="4978.9,221.5", + pos="e,4968.4,194.99 2640.8,251.71 2659.2,249.79 2678.4,248.08 2696.4,247 2933.6,232.77 4600.1,262.6 4835.4,229 4877.5,222.98 4923.8,\ +209.67 4958.5,198.29", style=solid]; subject -> object [label=relation, lp="919.39,134.5", @@ -252,11 +367,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="1722.4,265", + pos="2743.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1853.4,265", + pos="2874.4,265", width=2.0762]; } diff --git a/graphviz/entity_to_disease_association.svg b/graphviz/entity_to_disease_association.svg index c5b7fd7ff6..b26cf7b329 100644 --- a/graphviz/entity_to_disease_association.svg +++ b/graphviz/entity_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + entity to disease association - -entity to disease association + +entity to disease association @@ -24,8 +24,8 @@ entity to disease association->association - - + + is_a @@ -37,9 +37,9 @@ entity to disease association->id - - -id + + +id @@ -50,9 +50,9 @@ entity to disease association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ entity to disease association->name - - -name + + +name @@ -76,9 +76,9 @@ entity to disease association->description - - -description + + +description @@ -89,9 +89,9 @@ entity to disease association->has attribute - - -has attribute + + +has attribute @@ -102,8 +102,8 @@ entity to disease association->subject - - + + subject @@ -115,8 +115,8 @@ entity to disease association->predicate - - + + predicate @@ -128,7 +128,7 @@ entity to disease association->object - + object @@ -141,9 +141,9 @@ entity to disease association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ entity to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ entity to disease association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ entity to disease association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ entity to disease association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ entity to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ entity to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ entity to disease association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ entity to disease association->original subject - - -original subject + + +original subject @@ -258,98 +258,241 @@ entity to disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string entity to disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +entity to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +entity to disease association->object category + + +object category + + + +subject closure + +string + + + +entity to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +entity to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +entity to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +entity to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +entity to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +entity to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +entity to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +entity to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +entity to disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + entity to disease association->type - - -type + + +type - + category - -category + +category - + entity to disease association->category - - -category + + +category - + FDA approval status - -FDAApprovalStatusEnum + +FDAApprovalStatusEnum - + entity to disease association->FDA approval status - - -FDA approval status + + +FDA approval status - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/entity_to_phenotypic_feature_association.gv b/graphviz/entity_to_phenotypic_feature_association.gv index eb7baaf6fc..491adfc347 100644 --- a/graphviz/entity_to_phenotypic_feature_association.gv +++ b/graphviz/entity_to_phenotypic_feature_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3446.4,283"]; + graph [bb="0,0,5142.4,283"]; node [label="\N"]; "entity to phenotypic feature association" [height=0.5, label="entity to phenotypic feature association", - pos="1523.4,265", + pos="2544.4,265", width=5.4342]; association [height=0.5, pos="62.394,178", width=1.7332]; "entity to phenotypic feature association" -> association [label=is_a, lp="280.39,221.5", - pos="e,103.32,191.76 1328.3,263.62 1027.7,262.19 465.44,255.85 266.39,229 213.31,221.84 153.98,206.43 113.05,194.6"]; + pos="e,102.91,191.8 2349.2,263.52 1835.2,261.88 469.53,255.12 266.39,229 213.1,222.15 153.57,206.62 112.64,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "entity to phenotypic feature association" -> id [color=blue, label=id, - lp="397.39,221.5", - pos="e,210.38,189.99 1330.2,262.03 1055.7,258.54 566.43,249.61 390.39,229 317.85,220.51 299.77,215.57 229.39,196 226.29,195.14 223.09,\ -194.17 219.89,193.15", + lp="396.39,221.5", + pos="e,210.38,189.98 2350,262.92 1856.5,259.89 580.7,250.09 389.39,229 317.22,221.04 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "entity to phenotypic feature association" -> iri [color=blue, label=iri, - lp="513.39,221.5", - pos="e,315.3,190.22 1332.6,261.03 1083.2,256.52 660.02,246.56 505.39,229 428.92,220.32 409.95,215.12 335.39,196 332.02,195.13 328.54,\ -194.17 325.05,193.16", + lp="503.39,221.5", + pos="e,315.31,190.16 2350.1,262.74 1874.2,259.37 676.07,249 495.39,229 423.23,221.01 405.62,214.45 335.39,196 332.02,195.11 328.55,194.14 \ +325.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "entity to phenotypic feature association" -> name [color=blue, label=name, - lp="615.39,221.5", - pos="e,439.55,191.43 1331,261.6 1101.6,257.88 732.1,248.96 595.39,229 544.85,221.62 488.44,206.25 449.54,194.49", + lp="607.39,221.5", + pos="e,438.25,191.78 2349.4,263.22 1888.7,260.99 758.16,253.11 587.39,229 538.92,222.16 485.05,206.79 447.81,194.88", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "entity to phenotypic feature association" -> description [color=blue, label=description, - lp="729.89,221.5", - pos="e,584.6,194.29 1329,262.68 1121.6,260.05 807.14,252.23 689.39,229 656.44,222.5 620.84,209.44 594.05,198.29", + lp="723.89,221.5", + pos="e,582.77,194.4 2348.6,264.11 1903.8,263.8 843.19,259.81 683.39,229 651.71,222.89 617.7,209.84 592.13,198.6", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "entity to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="866.39,221.5", - pos="e,723.86,193.3 1331.1,261.66 1156.7,258.22 913.19,249.77 819.39,229 789.19,222.31 756.86,208.9 732.93,197.65", + lp="862.39,221.5", + pos="e,722.86,193.55 2348.7,264.18 1927.7,263.96 961.69,260.03 815.39,229 786.11,222.79 754.98,209.44 731.91,198.1", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { "entity to phenotypic feature association" -> subject [color=blue, label=subject, lp="989.39,221.5", - pos="e,867.11,194.24 1339.8,258.69 1204.6,253.61 1032.7,244.4 963.39,229 933.27,222.3 900.94,209.48 876.43,198.5", + pos="e,866.52,194.37 2349.3,263.52 1956.3,261.99 1095.6,255.61 963.39,229 932.94,222.87 900.37,209.91 875.84,198.72", style=solid]; predicate [color=blue, height=0.5, @@ -81,7 +81,7 @@ digraph { "entity to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1068.4,221.5", - pos="e,1008.5,195.95 1339.6,258.76 1212.2,253.78 1060.7,244.66 1034.4,229 1025.2,223.53 1018.2,214.26 1013.1,205.18", + pos="e,1008.4,196.14 2348.6,264.32 1952.9,264.31 1090.6,260.62 1034.4,229 1025,223.7 1017.9,214.33 1012.8,205.13", style=solid]; object [color=blue, height=0.5, @@ -91,7 +91,7 @@ digraph { "entity to phenotypic feature association" -> object [color=blue, label=object, lp="1147.4,178", - pos="e,976.03,105.47 1433.1,249.02 1396.3,242.87 1353.3,235.65 1314.4,229 1230.3,214.62 1201.1,235.31 1125.4,196 1105.3,185.57 1108.1,\ + pos="e,976.03,105.47 2352.7,261.26 2064.4,256.66 1532.5,246.16 1342.4,229 1245.2,220.23 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,\ 172.77 1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", style=solid]; negated [color=blue, @@ -101,8 +101,8 @@ digraph { width=1.2999]; "entity to phenotypic feature association" -> negated [color=blue, label=negated, - lp="1393.4,221.5", - pos="e,1256.5,191.48 1443.6,248.54 1418.1,243.04 1389.9,236.37 1364.4,229 1330.8,219.31 1293.6,205.77 1266.1,195.22", + lp="1452.4,221.5", + pos="e,1260,190.39 2350.6,262.52 2078.4,259.65 1596.8,251.49 1423.4,229 1369.6,222.02 1309.4,205.52 1269.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -111,8 +111,8 @@ digraph { width=2.1304]; "entity to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="1485.9,221.5", - pos="e,1392.9,195.02 1488.1,247.2 1476.6,241.58 1463.9,235.17 1452.4,229 1435.5,219.92 1417,209.3 1401.6,200.19", + lp="1585.9,221.5", + pos="e,1408.3,193.2 2350.7,262.38 2106.5,259.44 1700.8,251.27 1552.4,229 1506.1,222.05 1454.8,207.75 1417.8,196.22", style=solid]; publications [color=blue, height=0.5, @@ -121,8 +121,8 @@ digraph { width=1.7332]; "entity to phenotypic feature association" -> publications [color=blue, label=publications, - lp="1567.4,221.5", - pos="e,1523.4,196.18 1523.4,246.8 1523.4,235.16 1523.4,219.55 1523.4,206.24", + lp="1724.4,221.5", + pos="e,1558.3,193.08 2350.9,262.17 2136.4,259.08 1804.3,250.83 1680.4,229 1641.5,222.15 1598.9,208.14 1567.9,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -131,8 +131,8 @@ digraph { width=2.0943]; "entity to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="1684.9,221.5", - pos="e,1661.1,195.69 1574.8,247.56 1588.3,242.39 1602.7,236.13 1615.4,229 1628.7,221.48 1642.3,211.34 1653.5,202.15", + lp="1871.9,221.5", + pos="e,1714.3,194.09 2354.1,260.77 2175.9,256.64 1922.8,247.67 1825.4,229 1790.4,222.3 1752.4,209.09 1724,197.93", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -141,8 +141,8 @@ digraph { width=3.015]; "entity to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1848.9,221.5", - pos="e,1841.3,194.73 1630.3,249.9 1664.2,244.49 1701.6,237.52 1735.4,229 1768,220.77 1803.8,208.57 1831.8,198.28", + lp="2011.9,221.5", + pos="e,1897.9,195.96 2361.2,258.62 2200.1,253.01 1985.5,243.06 1947.4,229 1931.9,223.3 1917.1,212.69 1905.4,202.7", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -151,8 +151,8 @@ digraph { width=3.015]; "entity to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2084.4,221.5", - pos="e,2066.1,193.96 1661.7,252.23 1770.1,242.93 1904.6,231.16 1917.4,229 1964.7,221.01 2017.2,207.6 2056.5,196.68", + lp="2178.4,221.5", + pos="e,2094.1,195.74 2352.5,261.48 2234.5,257.88 2102.2,249.29 2083.4,229 2076.2,221.21 2080,211.68 2087.1,203.04", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -161,9 +161,8 @@ digraph { width=3.015]; "entity to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2350.9,221.5", - pos="e,2309.3,194.73 1658.4,251.97 1681.7,250.13 1705.8,248.39 1728.4,247 1930.4,234.63 1983.7,262.12 2183.4,229 2223.1,222.41 2266.7,\ -209.28 2299.5,198.12", + lp="2387.9,221.5", + pos="e,2304.5,194.27 2365.7,257.63 2327.2,252.43 2294.2,243.64 2281.4,229 2271.3,217.45 2280.6,207.11 2295.3,198.87", style=solid]; timepoint [color=blue, height=0.5, @@ -172,9 +171,8 @@ digraph { width=1.5346]; "entity to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="2526.4,221.5", - pos="e,2516.4,195.18 1656.7,251.81 1680.6,249.95 1705.2,248.24 1728.4,247 1809.7,242.63 2384,254.3 2461.4,229 2478.6,223.38 2495.4,212.19 \ -2508.4,201.81", + lp="2534.4,221.5", + pos="e,2512,194.95 2514.8,247.2 2508.6,242.2 2502.9,236.11 2499.4,229 2494.9,219.85 2498.7,210.46 2505.2,202.32", style=solid]; "original subject" [color=blue, height=0.5, @@ -183,9 +181,8 @@ digraph { width=1.0652]; "entity to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="2654.4,221.5", - pos="e,2627.7,194 1656.5,251.77 1680.4,249.91 1705.1,248.21 1728.4,247 1821.3,242.15 2476.3,255.6 2565.4,229 2585.1,223.13 2604.7,211.01 \ -2619.5,200.18", + lp="2648.4,221.5", + pos="e,2622.4,192.59 2559.1,246.86 2568.2,236.75 2580.4,224.01 2592.4,214 2599.1,208.42 2606.7,202.95 2614,198.05", style=solid]; "original predicate" [color=blue, height=0.5, @@ -194,49 +191,168 @@ digraph { width=1.5887]; "entity to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="2798.9,221.5", - pos="e,2749.5,195.82 1655.9,251.75 1680,249.88 1704.9,248.19 1728.4,247 1783.1,244.23 2664.6,251.75 2714.4,229 2726.1,223.68 2736,213.72 \ -2743.5,204.08", + lp="2789.9,221.5", + pos="e,2745.2,195.87 2647.9,249.67 2667.3,244.69 2687,238 2704.4,229 2716.9,222.55 2728.7,212.55 2738.2,203.17", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2909.4,178", + pos="2873.4,178", width=1.0652]; "entity to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="2937.9,221.5", - pos="e,2900.2,195.81 1655.6,251.73 1679.8,249.85 1704.9,248.16 1728.4,247 1760,245.44 2837.8,242.41 2866.4,229 2877.8,223.66 2887.3,213.7 \ -2894.5,204.07", + lp="2917.9,221.5", + pos="e,2871.5,196.07 2679.2,251.94 2759.4,244.24 2847.1,234.67 2854.4,229 2861.7,223.35 2866.2,214.58 2868.9,205.94", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3006.4,178", + width=2.1304]; + "entity to phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3048.9,221.5", + pos="e,2999.7,196.42 2684.2,252.36 2706,250.56 2728.3,248.72 2749.4,247 2799.2,242.94 2930.4,254.41 2973.4,229 2982.6,223.58 2989.7,214.49 \ +2994.9,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3177.4,178", + width=2.1304]; + "entity to phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3193.9,221.5", + pos="e,3161.5,195.76 2680.8,252.05 2703.7,250.23 2727.2,248.47 2749.4,247 2830,241.66 3036.6,256.89 3112.4,229 3127.8,223.33 3142.5,212.61 \ +3154.1,202.55", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3310.4,178", + width=1.0652]; + "entity to phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="3332.9,221.5", + pos="e,3297.3,195.32 2679.1,251.92 2702.5,250.08 2726.7,248.35 2749.4,247 2805.3,243.68 3201.3,249.67 3253.4,229 3267.4,223.43 3280.3,\ +212.8 3290.3,202.78", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3408.4,178", + width=1.0652]; + "entity to phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="3450.4,221.5", + pos="e,3406.3,196.37 2678.3,251.84 2702,249.99 2726.4,248.28 2749.4,247 2784.9,245.03 3359.3,249.32 3388.4,229 3396.1,223.64 3400.8,214.8 \ +3403.7,206.04", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3541.4,178", + width=2.1304]; + "entity to phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3608.9,221.5", + pos="e,3533.8,196.2 2677.7,251.8 2701.6,249.94 2726.2,248.24 2749.4,247 2791.3,244.77 3467.2,248.33 3504.4,229 3514.6,223.72 3522.7,214.23 \ +3528.7,204.93", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3731.4,178", + width=2.1304]; + "entity to phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="3798.9,221.5", + pos="e,3725.7,196.14 2677.2,251.74 2701.2,249.88 2726,248.19 2749.4,247 2775.8,245.66 3677.4,242.07 3700.4,229 3709.6,223.75 3716.5,214.53 \ +3721.3,205.42", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3921.4,178", + width=1.0652]; + "entity to phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3971.4,221.5", + pos="e,3914.4,196.21 2676.6,251.73 2700.8,249.85 2725.9,248.16 2749.4,247 2780.9,245.44 3858.5,243.81 3886.4,229 3896.2,223.78 3903.9,\ +214.44 3909.5,205.22", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4080.4,178", + width=1.0652]; + "entity to phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4124.4,221.5", + pos="e,4073,195.75 2676.4,251.71 2700.6,249.83 2725.8,248.14 2749.4,247 2785.3,245.26 4011.4,245.4 4043.4,229 4053.7,223.7 4061.9,214.02 \ +4067.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4231.4,178", + width=1.0652]; + "entity to phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4284.4,221.5", + pos="e,4223.4,195.78 2676.4,251.68 2700.6,249.81 2725.8,248.13 2749.4,247 2789.4,245.09 4156.5,246.81 4192.4,229 4203.1,223.68 4211.8,\ +213.86 4218.2,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4402.4,178", + width=1.0652]; + "entity to phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="4450.9,221.5", + pos="e,4394.1,195.8 2676.1,251.68 2700.4,249.8 2725.7,248.11 2749.4,247 2794.2,244.9 4322.1,248.64 4362.4,229 4373.3,223.7 4382.1,213.89 \ +4388.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4564.4,178", + width=2.347]; + "entity to phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4612.9,221.5", + pos="e,4555.8,196.3 2676.1,251.66 2700.4,249.78 2725.7,248.1 2749.4,247 2798.6,244.71 4480.1,250.58 4524.4,229 4535.1,223.78 4543.9,214.17 \ +4550.4,204.76", style=solid]; type [height=0.5, - pos="3016.4,178", + pos="4712.4,178", width=0.86659]; "entity to phenotypic feature association" -> type [color=blue, label=type, - lp="3022.4,221.5", - pos="e,3013.4,196 1655.6,251.69 1679.8,249.83 1704.9,248.14 1728.4,247 1763.5,245.3 2963.9,248.17 2993.4,229 3001.5,223.7 3006.8,214.72 \ -3010.3,205.81", + lp="4716.4,221.5", + pos="e,4708.4,196.08 2675.8,251.66 2700.2,249.78 2725.6,248.1 2749.4,247 2776.3,245.76 4663.5,243.07 4686.4,229 4695,223.74 4700.8,214.64 \ +4704.8,205.63", style=solid]; category [height=0.5, - pos="3117.4,178", + pos="4813.4,178", width=1.4263]; "entity to phenotypic feature association" -> category [color=blue, label=category, - lp="3105.9,221.5", - pos="e,3099.8,195.01 1655.4,251.71 1679.6,249.83 1704.8,248.14 1728.4,247 1801.3,243.48 2972.7,250.63 3042.4,229 3060.5,223.39 3078.2,\ -211.93 3091.9,201.39", + lp="4799.9,221.5", + pos="e,4795.3,195.04 2675.8,251.66 2700.2,249.77 2725.6,248.09 2749.4,247 2804.5,244.47 4683.5,244.92 4736.4,229 4754.8,223.44 4773,211.98 \ +4787.1,201.43", style=solid]; "FDA approval status" [color=blue, height=0.5, label=FDAApprovalStatusEnum, - pos="3316.4,178", + pos="5012.4,178", width=3.6108]; "entity to phenotypic feature association" -> "FDA approval status" [color=blue, label="FDA approval status", - lp="3283.9,221.5", - pos="e,3272.5,195.06 1655.4,251.69 1679.6,249.81 1704.8,248.13 1728.4,247 1885.2,239.51 2986,251.77 3141.4,229 3182.9,222.91 3228.5,209.67 \ -3262.7,198.35", + lp="4978.9,221.5", + pos="e,4968.4,194.98 2675.8,251.65 2700.2,249.77 2725.6,248.09 2749.4,247 2980.9,236.41 4605.9,261.8 4835.4,229 4877.5,222.98 4923.8,\ +209.66 4958.5,198.29", style=solid]; subject -> object [label=relation, lp="919.39,134.5", @@ -251,11 +367,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="1775.4,265", + pos="2796.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1906.4,265", + pos="2927.4,265", width=2.0762]; } diff --git a/graphviz/entity_to_phenotypic_feature_association.svg b/graphviz/entity_to_phenotypic_feature_association.svg index 23f5d37a7c..b85d8246a8 100644 --- a/graphviz/entity_to_phenotypic_feature_association.svg +++ b/graphviz/entity_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + entity to phenotypic feature association - -entity to phenotypic feature association + +entity to phenotypic feature association @@ -24,8 +24,8 @@ entity to phenotypic feature association->association - - + + is_a @@ -37,9 +37,9 @@ entity to phenotypic feature association->id - - -id + + +id @@ -50,9 +50,9 @@ entity to phenotypic feature association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ entity to phenotypic feature association->name - - -name + + +name @@ -76,9 +76,9 @@ entity to phenotypic feature association->description - - -description + + +description @@ -89,9 +89,9 @@ entity to phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -102,8 +102,8 @@ entity to phenotypic feature association->subject - - + + subject @@ -115,8 +115,8 @@ entity to phenotypic feature association->predicate - - + + predicate @@ -128,7 +128,7 @@ entity to phenotypic feature association->object - + object @@ -141,9 +141,9 @@ entity to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ entity to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ entity to phenotypic feature association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ entity to phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ entity to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ entity to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ entity to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ entity to phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ entity to phenotypic feature association->original subject - - -original subject + + +original subject @@ -258,98 +258,241 @@ entity to phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string entity to phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +entity to phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +entity to phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +entity to phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +entity to phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +entity to phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +entity to phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +entity to phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +entity to phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +entity to phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +entity to phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +entity to phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + entity to phenotypic feature association->type - - -type + + +type - + category - -category + +category - + entity to phenotypic feature association->category - - -category + + +category - + FDA approval status - -FDAApprovalStatusEnum + +FDAApprovalStatusEnum - + entity to phenotypic feature association->FDA approval status - - -FDA approval status + + +FDA approval status - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/exon_to_transcript_relationship.gv b/graphviz/exon_to_transcript_relationship.gv index 354e87c995..ae2e88c490 100644 --- a/graphviz/exon_to_transcript_relationship.gv +++ b/graphviz/exon_to_transcript_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3238.5,283"]; + graph [bb="0,0,4962.5,283"]; node [label="\N"]; "exon to transcript relationship" [height=0.5, label="exon to transcript relationship", - pos="1716.5,265", + pos="2666.5,265", width=4.2427]; "sequence feature relationship" [height=0.5, pos="149.49,178", width=4.1524]; "exon to transcript relationship" -> "sequence feature relationship" [label=is_a, - lp="457.49,221.5", - pos="e,220.1,193.89 1565.1,262.51 1276.3,259.24 656.64,249.95 443.49,229 370.79,221.85 288.92,207.4 230.08,195.86"]; + lp="455.49,221.5", + pos="e,219,194.01 2514.5,262.97 2046.5,259.59 646.03,248.01 441.49,229 368.99,222.26 287.38,207.69 228.91,196"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "exon to transcript relationship" -> id [color=blue, label=id, - lp="577.49,221.5", - pos="e,384.21,189.94 1565.2,262.47 1299.3,259.27 758.51,250.3 570.49,229 495.31,220.48 476.45,216.02 403.49,196 400.33,195.13 397.09,\ -194.16 393.84,193.14", + lp="572.49,221.5", + pos="e,384.47,190 2514.3,263.09 2063.9,260.15 757.07,249.93 565.49,229 492.44,221.02 474.29,215.65 403.49,196 400.38,195.14 397.18,194.17 \ +393.98,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "exon to transcript relationship" -> iri [color=blue, label=iri, - lp="701.49,221.5", - pos="e,489.09,190.21 1566.2,261.51 1324,257.04 857.94,246.47 693.49,229 610.87,220.22 590.11,216.07 509.49,196 506.05,195.15 502.52,194.19 \ -498.98,193.17", + lp="689.49,221.5", + pos="e,489.39,190.23 2514.7,262.83 2081.9,259.28 861.47,247.71 681.49,229 604.07,220.95 584.91,215.26 509.49,196 506.11,195.14 502.63,\ +194.18 499.14,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "exon to transcript relationship" -> name [color=blue, label=name, - lp="810.49,221.5", - pos="e,615.46,190.85 1566.4,261.61 1343.6,257.51 935.89,247.69 790.49,229 733.01,221.61 668.41,205.5 625.17,193.56", + lp="801.49,221.5", + pos="e,614.11,191.15 2514.5,263.04 2096.7,260.13 950.92,250.29 781.49,229 726.67,222.11 665.3,206.11 623.92,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "exon to transcript relationship" -> description [color=blue, label=description, - lp="935.99,221.5", - pos="e,764.69,193.5 1565.8,261.96 1364.8,258.48 1020,249.65 895.49,229 853.78,222.08 807.86,208.18 774.27,196.79", + lp="929.99,221.5", + pos="e,762.9,193.65 2514.2,263.41 2113,261.5 1047.3,254.11 889.49,229 849.13,222.58 804.89,208.66 772.54,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "exon to transcript relationship" -> "has attribute" [color=blue, label="has attribute", - lp="1089.5,221.5", - pos="e,904.86,191.55 1569,260.31 1401.8,255.44 1140,245.47 1042.5,229 998.11,221.5 948.94,206.5 914.58,194.88", + lp="1087.5,221.5", + pos="e,904.07,191.75 2514.6,263.02 2138.4,260.26 1183.4,251.15 1040.5,229 996.35,222.16 947.61,207 913.67,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "exon to transcript relationship" -> predicate [color=blue, label=predicate, - lp="1242.5,221.5", - pos="e,1062.1,193 1567.3,261.11 1465.6,257.33 1328.2,248.7 1208.5,229 1161.7,221.3 1109.7,207.21 1071.9,195.94", + lp="1248.5,221.5", + pos="e,1061.9,193.09 2513.5,264.67 2193.3,265.37 1461.5,263.03 1214.5,229 1165.3,222.22 1110.6,207.65 1071.5,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "exon to transcript relationship" -> negated [color=blue, label=negated, - lp="1375.5,221.5", - pos="e,1195.8,190.34 1582.2,256.31 1511.7,251.01 1424.1,242.43 1346.5,229 1297.6,220.54 1243,204.99 1205.8,193.47", + lp="1394.5,221.5", + pos="e,1196.4,190.23 2514.2,263.55 2220,262.08 1583.4,255.81 1365.5,229 1309.6,222.13 1247,205.38 1206.1,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "exon to transcript relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1495,221.5", - pos="e,1342.2,193.53 1604.4,252.74 1559.6,247.18 1507.8,239.39 1461.5,229 1424.2,220.63 1383,207.57 1351.9,196.9", + lp="1531,221.5", + pos="e,1345.7,193.02 2513.9,263.62 2243.2,262.24 1689,256.09 1497.5,229 1448.7,222.11 1394.6,207.65 1355.7,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "exon to transcript relationship" -> publications [color=blue, label=publications, - lp="1612.5,221.5", - pos="e,1488.4,194.2 1641.5,249.3 1617.9,243.86 1591.8,237.03 1568.5,229 1544.2,220.66 1518.1,208.78 1497.5,198.69", + lp="1673.5,221.5", + pos="e,1496,192.66 2513.9,263.57 2268,262.07 1795,255.69 1629.5,229 1586.6,222.09 1539.4,207.61 1505.6,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "exon to transcript relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1719,221.5", - pos="e,1635.2,195.6 1696,246.8 1680.8,233.96 1659.8,216.27 1643,202.19", + lp="1827,221.5", + pos="e,1653.5,193.55 2514.7,262.66 2299.6,259.97 1917.1,252.01 1780.5,229 1740.1,222.2 1695.7,208.38 1663.2,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "exon to transcript relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1850,221.5", - pos="e,1802.8,196.14 1744.5,247.13 1752.9,241.7 1761.8,235.42 1769.5,229 1778.7,221.33 1788,212.07 1795.9,203.61", + lp="1977,221.5", + pos="e,1842,195.78 2513.4,264.72 2326.4,264.24 2021.6,258.67 1912.5,229 1890.7,223.09 1868.3,211.61 1850.8,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "exon to transcript relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2058.5,221.5", - pos="e,2015.3,195.02 1813.1,251 1846.8,245.49 1884.6,238.18 1918.5,229 1948.1,220.97 1980.4,209.03 2005.9,198.83", + lp="2146.5,221.5", + pos="e,2046.7,196 2518.3,260.62 2341.5,255.84 2067.3,245.77 2051.5,229 2045.7,222.9 2044.5,214.27 2045.1,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "exon to transcript relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2312,221.5", - pos="e,2253.9,195.18 1823.6,252.15 1841.9,250.3 1860.7,248.5 1878.5,247 2002.3,236.51 2036.1,255.61 2157.5,229 2187.5,222.41 2219.8,210.02 \ -2244.7,199.22", + lp="2355,221.5", + pos="e,2261.7,195.53 2516.9,261.19 2404.5,257.49 2266.8,248.9 2248.5,229 2240.8,220.62 2245.7,210.86 2254.2,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "exon to transcript relationship" -> timepoint [color=blue, label=timepoint, - lp="2477.5,221.5", - pos="e,2459,195.77 1821.4,251.89 1840.4,250.01 1860,248.27 1878.5,247 1938.8,242.84 2367.4,253.92 2422.5,229 2434.5,223.55 2445,213.44 \ -2452.9,203.72", + lp="2506.5,221.5", + pos="e,2465.2,196.26 2543.5,254.29 2511.1,249.1 2482.1,241.16 2471.5,229 2466.1,222.83 2464.4,214.43 2464.4,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "exon to transcript relationship" -> "original subject" [color=blue, label="original subject", - lp="2596.5,221.5", - pos="e,2564.3,194.22 1821,251.85 1840.1,249.97 1859.9,248.24 1878.5,247 1949.2,242.3 2449.7,252.78 2516.5,229 2525.3,225.86 2542.2,212.73 \ -2556.6,200.71", + lp="2604.5,221.5", + pos="e,2561.4,193.75 2575.2,250.43 2564.8,245.28 2555.5,238.33 2548.5,229 2541.8,220.01 2546.6,209.73 2554.4,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,203 @@ digraph { width=1.5887]; "exon to transcript relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2737,221.5", - pos="e,2686.9,196.24 1820.5,251.82 1839.8,249.92 1859.7,248.2 1878.5,247 1921.6,244.24 2616.8,248.15 2655.5,229 2666.2,223.71 2674.9,\ -214.09 2681.5,204.69", + lp="2731,221.5", + pos="e,2678.7,195.4 2664.1,246.84 2663.5,236.95 2663.7,224.45 2667.5,214 2668.8,210.42 2670.6,206.94 2672.7,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2827.5,178", + pos="2809.5,178", width=1.0652]; "exon to transcript relationship" -> "original object" [color=blue, label="original object", - lp="2869,221.5", - pos="e,2824.5,195.98 1820.5,251.76 1839.8,249.87 1859.7,248.17 1878.5,247 1904.2,245.41 2783,243.09 2804.5,229 2812.6,223.68 2817.9,214.69 \ -2821.4,205.79", + lp="2856,221.5", + pos="e,2808.4,196.46 2759.6,250.71 2772.5,245.59 2784.7,238.57 2794.5,229 2800.6,223.04 2804.2,214.69 2806.4,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2942.5,178", + width=2.1304]; + "exon to transcript relationship" -> "subject category" [color=blue, + label="subject category", + lp="2986,221.5", + pos="e,2936.3,196.16 2776.9,252.54 2836.3,245.61 2899.8,236.67 2911.5,229 2920.2,223.28 2927,214.13 2931.9,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3113.5,178", + width=2.1304]; + "exon to transcript relationship" -> "object category" [color=blue, + label="object category", + lp="3131,221.5", + pos="e,3097.6,195.83 2774.9,252.27 2792.8,250.43 2811.2,248.61 2828.5,247 2877.5,242.43 3003.6,246.92 3049.5,229 3064.4,223.18 3078.7,\ +212.7 3089.9,202.83", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3246.5,178", + width=1.0652]; + "exon to transcript relationship" -> "subject closure" [color=blue, + label="subject closure", + lp="3268,221.5", + pos="e,3233.7,195.25 2772.7,252.01 2791.3,250.15 2810.4,248.39 2828.5,247 2868.6,243.9 3153.2,244.28 3190.5,229 3204.3,223.32 3217,212.69 \ +3226.8,202.68", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3346.5,178", + width=1.0652]; + "exon to transcript relationship" -> "object closure" [color=blue, + label="object closure", + lp="3388.5,221.5", + pos="e,3344.4,196.34 2771.8,251.89 2790.7,250.02 2810.2,248.29 2828.5,247 2856.1,245.05 3303.8,244.93 3326.5,229 3334.2,223.61 3338.9,\ +214.77 3341.8,206.01", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3479.5,178", + width=2.1304]; + "exon to transcript relationship" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3547,221.5", + pos="e,3471.8,196.18 2771.4,251.83 2790.4,249.96 2810,248.24 2828.5,247 2862.5,244.72 3412.2,244.8 3442.5,229 3452.6,223.69 3460.7,214.2 \ +3466.7,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3671.5,178", + width=2.1304]; + "exon to transcript relationship" -> "object category closure" [color=blue, + label="object category closure", + lp="3738,221.5", + pos="e,3665.2,196.16 2770.5,251.8 2789.8,249.91 2809.7,248.19 2828.5,247 2873.4,244.15 3599.1,250.77 3638.5,229 3648,223.72 3655.3,214.36 \ +3660.6,205.15", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3861.5,178", + width=1.0652]; + "exon to transcript relationship" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3910.5,221.5", + pos="e,3854.4,195.72 2770.5,251.74 2789.8,249.85 2809.7,248.15 2828.5,247 2883.8,243.61 3776.4,254.7 3825.5,229 3835.7,223.66 3843.7,\ +213.97 3849.5,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4020.5,178", + width=1.0652]; + "exon to transcript relationship" -> "object namespace" [color=blue, + label="object namespace", + lp="4064.5,221.5", + pos="e,4012.8,195.76 2770.1,251.74 2789.5,249.84 2809.6,248.14 2828.5,247 2860.5,245.08 3953.9,243.47 3982.5,229 3993,223.7 4001.3,214.03 \ +4007.5,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4171.5,178", + width=1.0652]; + "exon to transcript relationship" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4224.5,221.5", + pos="e,4163.5,195.78 2770.1,251.72 2789.5,249.82 2809.6,248.12 2828.5,247 2864.6,244.86 4100,245.12 4132.5,229 4143.2,223.67 4151.9,213.85 \ +4158.3,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4342.5,178", + width=1.0652]; + "exon to transcript relationship" -> "object label closure" [color=blue, + label="object label closure", + lp="4390,221.5", + pos="e,4334.2,195.8 2770.1,251.69 2789.5,249.8 2809.6,248.11 2828.5,247 2869.4,244.61 4265.7,246.96 4302.5,229 4313.3,223.7 4322.2,213.88 \ +4328.8,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4504.5,178", + width=2.347]; + "exon to transcript relationship" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4553,221.5", + pos="e,4495.6,196.31 2769.6,251.72 2789.2,249.81 2809.4,248.1 2828.5,247 2873.8,244.38 4422.5,248.65 4463.5,229 4474.3,223.79 4483.3,\ +214.18 4490,204.77", style=solid]; type [height=0.5, - pos="2915.5,178", + pos="4638.5,178", width=0.86659]; "exon to transcript relationship" -> type [color=blue, label=type, - lp="2946.5,221.5", - pos="e,2924.9,195.54 1820.1,251.77 1839.5,249.87 1859.6,248.15 1878.5,247 1907.5,245.23 2904.1,249.72 2924.5,229 2930.7,222.69 2930.6,\ -213.66 2928.3,205", + lp="4652.5,221.5", + pos="e,4639.3,196.18 2769.6,251.7 2789.2,249.79 2809.4,248.09 2828.5,247 2853.4,245.57 4607,244.56 4626.5,229 4633.3,223.54 4636.7,214.93 \ +4638.2,206.37", style=solid]; category [height=0.5, - pos="3016.5,178", + pos="4739.5,178", width=1.4263]; "exon to transcript relationship" -> category [color=blue, label=category, - lp="3021,221.5", - pos="e,3005.1,195.87 1820.1,251.76 1839.5,249.86 1859.6,248.15 1878.5,247 1938.8,243.34 2910.8,252.6 2966.5,229 2979,223.68 2990.1,213.59 \ -2998.6,203.85", + lp="4733,221.5", + pos="e,4723.9,195.25 2769.6,251.7 2789.2,249.79 2809.4,248.09 2828.5,247 2879.6,244.07 4624,245.38 4672.5,229 4688.7,223.53 4704.2,212.51 \ +4716.2,202.2", style=solid]; subject [height=0.5, - pos="3130.5,178", + pos="4853.5,178", width=1.2277]; "exon to transcript relationship" -> subject [color=blue, label=subject, - lp="3113.5,221.5", - pos="e,3113.5,194.76 1820.1,251.74 1839.5,249.84 1859.6,248.13 1878.5,247 1943.8,243.08 2994.1,248.64 3056.5,229 3074.5,223.34 3092.1,\ -211.75 3105.6,201.16", + lp="4829.5,221.5", + pos="e,4834.2,194.33 2769.6,251.69 2789.2,249.78 2809.4,248.09 2828.5,247 2936.1,240.87 4664.6,257.8 4768.5,229 4789.2,223.25 4810.1,\ +211.09 4826,200.2", style=solid]; object [height=0.5, - pos="3173.5,91", + pos="4896.5,91", width=1.0832]; "exon to transcript relationship" -> object [color=blue, label=object, - lp="3216.5,178", - pos="e,3186.9,108.09 1820.1,251.72 1839.5,249.83 1859.6,248.12 1878.5,247 1948.6,242.83 3077.5,253.23 3143.5,229 3186,213.39 3191.2,186.96 \ -3196.5,142 3197.3,135.38 3198.4,133.39 3196.5,127 3195.5,123.55 3194,120.13 3192.2,116.85", + lp="4940.5,178", + pos="e,4909.9,108.09 2769.6,251.68 2789.2,249.78 2809.4,248.08 2828.5,247 2884.8,243.8 4805.8,246.24 4859.5,229 4883.8,221.2 4892.1,217.1 \ +4906.5,196 4920.4,175.59 4916.6,166.51 4919.5,142 4920.3,135.38 4921.4,133.39 4919.5,127 4918.5,123.55 4917,120.13 4915.2,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1925.5,265", + pos="2875.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2056.5,265", + pos="3006.5,265", width=2.0762]; subject -> object [label=relation, - lp="3168.5,134.5", - pos="e,3155.6,107.23 3131.6,159.55 3132.8,149.57 3135.3,137.07 3140.5,127 3142.7,122.68 3145.6,118.52 3148.8,114.66"]; + lp="4891.5,134.5", + pos="e,4878.6,107.23 4854.6,159.55 4855.8,149.57 4858.3,137.07 4863.5,127 4865.7,122.68 4868.6,118.52 4871.8,114.66"]; relation [height=0.5, - pos="3118.5,18", + pos="4841.5,18", width=1.2999]; - subject -> relation [pos="e,3119.8,36.188 3129.2,159.79 3127.1,132.48 3123,78.994 3120.6,46.38", + subject -> relation [pos="e,4842.8,36.188 4852.2,159.79 4850.1,132.48 4846,78.994 4843.6,46.38", style=dotted]; "exon to transcript relationship_subject" [color=blue, height=0.5, label=exon, - pos="2181.5,265", + pos="3131.5,265", width=0.9027]; - object -> relation [pos="e,3131.3,35.54 3161,73.889 3154.1,64.939 3145.3,53.617 3137.5,43.584", + object -> relation [pos="e,4854.3,35.54 4884,73.889 4877.1,64.939 4868.3,53.617 4860.5,43.584", style=dotted]; "exon to transcript relationship_object" [color=blue, height=0.5, label=transcript, - pos="2289.5,265", + pos="3239.5,265", width=1.5887]; } diff --git a/graphviz/exon_to_transcript_relationship.svg b/graphviz/exon_to_transcript_relationship.svg index e9178d9582..e0e11ee383 100644 --- a/graphviz/exon_to_transcript_relationship.svg +++ b/graphviz/exon_to_transcript_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + exon to transcript relationship - -exon to transcript relationship + +exon to transcript relationship @@ -24,9 +24,9 @@ exon to transcript relationship->sequence feature relationship - - -is_a + + +is_a @@ -37,9 +37,9 @@ exon to transcript relationship->id - - -id + + +id @@ -50,9 +50,9 @@ exon to transcript relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ exon to transcript relationship->name - - -name + + +name @@ -76,9 +76,9 @@ exon to transcript relationship->description - - -description + + +description @@ -89,9 +89,9 @@ exon to transcript relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ exon to transcript relationship->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ exon to transcript relationship->negated - - -negated + + +negated @@ -128,9 +128,9 @@ exon to transcript relationship->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ exon to transcript relationship->publications - - -publications + + +publications @@ -154,9 +154,9 @@ exon to transcript relationship->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ exon to transcript relationship->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ exon to transcript relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ exon to transcript relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ exon to transcript relationship->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ exon to transcript relationship->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ exon to transcript relationship->original predicate - - -original predicate + + +original predicate original object - -string + +string exon to transcript relationship->original object - - -original object + + +original object - + +subject category + +ontology class + + + +exon to transcript relationship->subject category + + +subject category + + + +object category + +ontology class + + + +exon to transcript relationship->object category + + +object category + + + +subject closure + +string + + + +exon to transcript relationship->subject closure + + +subject closure + + + +object closure + +string + + + +exon to transcript relationship->object closure + + +object closure + + + +subject category closure + +ontology class + + + +exon to transcript relationship->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +exon to transcript relationship->object category closure + + +object category closure + + + +subject namespace + +string + + + +exon to transcript relationship->subject namespace + + +subject namespace + + + +object namespace + +string + + + +exon to transcript relationship->object namespace + + +object namespace + + + +subject label closure + +string + + + +exon to transcript relationship->subject label closure + + +subject label closure + + + +object label closure + +string + + + +exon to transcript relationship->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +exon to transcript relationship->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + exon to transcript relationship->type - - -type + + +type - + category - -category + +category - + exon to transcript relationship->category - - -category + + +category - + subject - -subject + +subject - + exon to transcript relationship->subject - - -subject + + +subject - + object - -object + +object - + exon to transcript relationship->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + exon to transcript relationship_subject - -exon + +exon - + object->relation - - + + - + exon to transcript relationship_object - -transcript + +transcript diff --git a/graphviz/exposure_event_to_outcome_association.gv b/graphviz/exposure_event_to_outcome_association.gv index 8564018447..044f7363a7 100644 --- a/graphviz/exposure_event_to_outcome_association.gv +++ b/graphviz/exposure_event_to_outcome_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,4021.4,283"]; + graph [bb="0,0,5734.4,283"]; node [label="\N"]; "exposure event to outcome association" [height=0.5, label="exposure event to outcome association", - pos="1893.4,265", + pos="2911.4,265", width=5.3079]; association [height=0.5, pos="62.394,178", width=1.7332]; "exposure event to outcome association" -> association [label=is_a, - lp="501.39,221.5", - pos="e,107.14,190.58 1703,263.38 1432.6,261.57 921.72,254.68 487.39,229 330.1,219.7 289.89,221.5 134.39,196 128.71,195.07 122.81,193.94 \ -116.94,192.72"]; + lp="493.39,221.5", + pos="e,107.14,190.56 2720.8,263.25 2227,261 914.2,252.88 479.39,229 325.59,220.55 286.37,221.09 134.39,196 128.71,195.06 122.81,193.93 \ +116.94,192.7"]; "entity to outcome association mixin" [height=0.5, pos="319.39,178", width=4.8926]; "exposure event to outcome association" -> "entity to outcome association mixin" [label=uses, lp="647.89,221.5", - pos="e,396.29,194.21 1705,261.81 1405.5,257.81 833.8,247.94 631.39,229 554.95,221.85 468.84,207.57 406.48,196.1"]; + pos="e,395.31,194.3 2720.2,264.6 2247.8,265.51 1034.5,264.21 631.39,229 554.52,222.29 467.92,207.85 405.5,196.21"]; id [color=blue, height=0.5, label=string, @@ -25,8 +25,8 @@ digraph { width=1.0652]; "exposure event to outcome association" -> id [color=blue, label=id, - lp="767.39,221.5", - pos="e,580.38,189.99 1704.8,262.09 1431.1,258.64 937.41,249.72 760.39,229 687.85,220.51 669.77,215.57 599.39,196 596.29,195.14 593.09,\ + lp="766.39,221.5", + pos="e,580.38,189.98 2721.3,262.94 2231.5,259.93 950.96,250.12 759.39,229 687.22,221.04 669.34,215.5 599.39,196 596.29,195.13 593.09,\ 194.17 589.89,193.15", style=solid]; iri [color=blue, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "exposure event to outcome association" -> iri [color=blue, label=iri, - lp="883.39,221.5", - pos="e,685.3,190.22 1706.8,261.1 1458,256.63 1030.9,246.66 875.39,229 798.92,220.32 779.95,215.12 705.39,196 702.02,195.13 698.54,194.17 \ -695.05,193.16", + lp="873.39,221.5", + pos="e,685.31,190.16 2721.7,262.77 2249.5,259.43 1046.4,249.03 865.39,229 793.23,221.01 775.62,214.45 705.39,196 702.02,195.11 698.55,\ +194.14 695.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "exposure event to outcome association" -> name [color=blue, label=name, - lp="985.39,221.5", - pos="e,809.55,191.43 1705.5,261.67 1476.5,258 1103,249.09 965.39,229 914.85,221.62 858.44,206.25 819.54,194.49", + lp="977.39,221.5", + pos="e,808.25,191.78 2721,263.24 2263.6,261.02 1128.4,253.15 957.39,229 908.92,222.16 855.05,206.78 817.81,194.88", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "exposure event to outcome association" -> description [color=blue, label=description, - lp="1099.9,221.5", - pos="e,954.6,194.29 1703.7,262.74 1496.4,260.17 1178,252.4 1059.4,229 1026.4,222.5 990.84,209.44 964.05,198.29", + lp="1093.9,221.5", + pos="e,952.77,194.4 2720.4,264.1 2279,263.81 1213.5,259.86 1053.4,229 1021.7,222.89 987.7,209.84 962.13,198.6", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "exposure event to outcome association" -> "has attribute" [color=blue, label="has attribute", - lp="1236.4,221.5", - pos="e,1093.9,193.3 1705.2,261.74 1530.6,258.36 1283.9,249.93 1189.4,229 1159.2,222.31 1126.9,208.9 1102.9,197.65", + lp="1232.4,221.5", + pos="e,1092.9,193.55 2720.4,264.17 2302.4,263.96 1331.9,260.09 1185.4,229 1156.1,222.79 1125,209.44 1101.9,198.1", style=solid]; subject [color=blue, height=0.5, @@ -78,7 +78,7 @@ digraph { "exposure event to outcome association" -> subject [color=blue, label=subject, lp="1359.4,221.5", - pos="e,1237.1,194.24 1713.6,258.83 1577.9,253.79 1403.3,244.55 1333.4,229 1303.3,222.3 1270.9,209.48 1246.4,198.5", + pos="e,1236.5,194.37 2720.8,263.53 2330.5,262.01 1465.8,255.65 1333.4,229 1302.9,222.87 1270.4,209.91 1245.8,198.72", style=solid]; predicate [color=blue, height=0.5, @@ -88,7 +88,7 @@ digraph { "exposure event to outcome association" -> predicate [color=blue, label=predicate, lp="1438.4,221.5", - pos="e,1378.5,195.95 1713.3,258.9 1585.1,253.95 1431,244.81 1404.4,229 1395.2,223.53 1388.2,214.26 1383.1,205.18", + pos="e,1378.4,196.14 2720.1,264.31 2327.1,264.31 1460.7,260.67 1404.4,229 1395,223.7 1387.9,214.33 1382.8,205.13", style=solid]; object [color=blue, height=0.5, @@ -98,7 +98,7 @@ digraph { "exposure event to outcome association" -> object [color=blue, label=object, lp="1517.4,178", - pos="e,1346,105.47 1803.6,249.11 1766.7,242.94 1723.5,235.68 1684.4,229 1600.3,214.62 1571.1,235.31 1495.4,196 1475.3,185.57 1478.1,172.77 \ + pos="e,1346,105.47 2724.3,261.32 2437.7,256.74 1902.9,246.21 1712.4,229 1615.2,220.23 1582.5,240.02 1495.4,196 1475.2,185.79 1478.1,172.77 \ 1459.4,160 1427.3,138.07 1387,120.64 1355.5,108.92", style=solid]; negated [color=blue, @@ -108,8 +108,8 @@ digraph { width=1.2999]; "exposure event to outcome association" -> negated [color=blue, label=negated, - lp="1763.4,221.5", - pos="e,1626.5,191.48 1813.6,248.54 1788.1,243.04 1759.9,236.37 1734.4,229 1700.8,219.31 1663.6,205.77 1636.1,195.22", + lp="1822.4,221.5", + pos="e,1630,190.39 2722.1,262.55 2451.4,259.7 1967.1,251.55 1793.4,229 1739.6,222.02 1679.4,205.52 1639.6,193.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -118,8 +118,8 @@ digraph { width=2.1304]; "exposure event to outcome association" -> qualifiers [color=blue, label=qualifiers, - lp="1855.9,221.5", - pos="e,1762.9,195.02 1858.1,247.2 1846.6,241.58 1833.9,235.17 1822.4,229 1805.5,219.92 1787,209.3 1771.6,200.19", + lp="1955.9,221.5", + pos="e,1778.3,193.2 2722.2,262.41 2479.2,259.49 2071.2,251.33 1922.4,229 1876.1,222.05 1824.8,207.75 1787.8,196.22", style=solid]; publications [color=blue, height=0.5, @@ -128,8 +128,8 @@ digraph { width=1.7332]; "exposure event to outcome association" -> publications [color=blue, label=publications, - lp="1937.4,221.5", - pos="e,1893.4,196.18 1893.4,246.8 1893.4,235.16 1893.4,219.55 1893.4,206.24", + lp="2093.4,221.5", + pos="e,1928,193.08 2722.1,262.25 2508.3,259.23 2173.7,251.03 2049.4,229 2010.7,222.15 1968.4,208.15 1937.6,196.7", style=solid]; "has evidence" [color=blue, height=0.5, @@ -138,8 +138,8 @@ digraph { width=2.0943]; "exposure event to outcome association" -> "has evidence" [color=blue, label="has evidence", - lp="2054.9,221.5", - pos="e,2031.1,195.69 1944.8,247.56 1958.3,242.39 1972.7,236.13 1985.4,229 1998.7,221.48 2012.3,211.34 2023.5,202.15", + lp="2239.9,221.5", + pos="e,2083.8,194.09 2725.1,260.93 2547,256.91 2291.3,247.98 2193.4,229 2158.9,222.31 2121.4,209.1 2093.3,197.94", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -148,8 +148,8 @@ digraph { width=3.015]; "exposure event to outcome association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2218.9,221.5", - pos="e,2211.3,194.73 1999.5,250.03 2033.6,244.6 2071.3,237.59 2105.4,229 2138,220.77 2173.8,208.57 2201.8,198.28", + lp="2378.9,221.5", + pos="e,2267,195.95 2731.2,258.92 2569.8,253.47 2352.6,243.58 2314.4,229 2299.6,223.35 2285.5,212.89 2274.5,202.99", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -158,8 +158,8 @@ digraph { width=3.015]; "exposure event to outcome association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2454.4,221.5", - pos="e,2436.1,193.96 2029.8,252.39 2138.5,243.07 2274.6,231.17 2287.4,229 2334.7,221.01 2387.2,207.6 2426.5,196.68", + lp="2545.4,221.5", + pos="e,2462.2,195.77 2723.7,261.61 2604.6,258.08 2469.4,249.53 2450.4,229 2443,220.97 2447.2,211.37 2455,202.74", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -168,9 +168,8 @@ digraph { width=3.015]; "exposure event to outcome association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2720.9,221.5", - pos="e,2679.6,194.62 2025.1,251.94 2047.9,250.11 2071.3,248.37 2093.4,247 2297.6,234.33 2351.5,262.44 2553.4,229 2593.3,222.4 2637,209.19 \ -2669.8,198.01", + lp="2754.9,221.5", + pos="e,2672.2,194.17 2735.1,257.95 2695.6,252.79 2661.5,243.94 2648.4,229 2638,217.1 2647.7,206.69 2663.1,198.49", style=solid]; timepoint [color=blue, height=0.5, @@ -179,9 +178,8 @@ digraph { width=1.5346]; "exposure event to outcome association" -> timepoint [color=blue, label=timepoint, - lp="2896.4,221.5", - pos="e,2886.4,195.18 2023.5,251.8 2046.8,249.94 2070.8,248.24 2093.4,247 2175.3,242.52 2753.4,254.47 2831.4,229 2848.6,223.38 2865.4,\ -212.19 2878.4,201.82", + lp="2901.4,221.5", + pos="e,2880.6,194.47 2881.8,247.2 2875.6,242.2 2869.9,236.11 2866.4,229 2861.7,219.42 2866.1,209.79 2873.4,201.57", style=solid]; "original subject" [color=blue, height=0.5, @@ -190,9 +188,8 @@ digraph { width=1.0652]; "exposure event to outcome association" -> "original subject" [color=blue, label="original subject", - lp="3024.4,221.5", - pos="e,2997.7,194 2023.2,251.76 2046.6,249.9 2070.7,248.21 2093.4,247 2186.8,242.03 2845.7,255.76 2935.4,229 2955.1,223.13 2974.7,211.01 \ -2989.5,200.18", + lp="3015.4,221.5", + pos="e,2991.4,192.24 2926,246.75 2935.1,236.6 2947.3,223.86 2959.4,214 2966.6,208.17 2974.8,202.54 2982.7,197.56", style=solid]; "original predicate" [color=blue, height=0.5, @@ -201,60 +198,179 @@ digraph { width=1.5887]; "exposure event to outcome association" -> "original predicate" [color=blue, label="original predicate", - lp="3168.9,221.5", - pos="e,3119.5,195.82 2022.7,251.74 2046.2,249.87 2070.5,248.18 2093.4,247 2148.4,244.17 3034.3,251.86 3084.4,229 3096.1,223.68 3106,213.72 \ -3113.5,204.08", + lp="3157.9,221.5", + pos="e,3114.2,195.85 3013,249.72 3033,244.74 3053.3,238.02 3071.4,229 3084.5,222.46 3097,212.32 3107.1,202.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3261.4,178", + pos="3243.4,178", width=1.0652]; "exposure event to outcome association" -> "original object" [color=blue, label="original object", - lp="3301.9,221.5", - pos="e,3257.7,196.04 2022.4,251.72 2046,249.85 2070.4,248.16 2093.4,247 2125.1,245.4 3209.5,245.91 3236.4,229 3244.8,223.69 3250.5,214.58 \ -3254.3,205.58", + lp="3285.9,221.5", + pos="e,3240.4,196.13 3044.4,251.99 3125,244.2 3213.9,234.52 3221.4,229 3229.1,223.36 3234.1,214.47 3237.4,205.74", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3376.4,178", + width=2.1304]; + "exposure event to outcome association" -> "subject category" [color=blue, + label="subject category", + lp="3416.9,221.5", + pos="e,3369.3,195.96 3047.2,252.33 3068.7,250.52 3090.6,248.69 3111.4,247 3162.5,242.83 3296.9,254.43 3341.4,229 3351.1,223.48 3358.7,\ +214.08 3364.3,204.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3547.4,178", + width=2.1304]; + "exposure event to outcome association" -> "object category" [color=blue, + label="object category", + lp="3562.9,221.5", + pos="e,3530.9,195.77 3044.2,252.04 3066.6,250.21 3089.7,248.45 3111.4,247 3193.3,241.52 3403.1,256.76 3480.4,229 3496.2,223.34 3511.3,\ +212.62 3523.2,202.56", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3680.4,178", + width=1.0652]; + "exposure event to outcome association" -> "subject closure" [color=blue, + label="subject closure", + lp="3698.9,221.5", + pos="e,3664.6,194.71 3042.8,251.89 3065.7,250.06 3089.2,248.33 3111.4,247 3168.1,243.59 3569.5,249.72 3622.4,229 3630.3,225.91 3644.7,\ +213.49 3657.2,201.8", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3776.4,178", + width=1.0652]; + "exposure event to outcome association" -> "object closure" [color=blue, + label="object closure", + lp="3818.4,221.5", + pos="e,3774,196.4 3042,251.82 3065.1,249.97 3089,248.27 3111.4,247 3147.1,244.98 3725.9,249.23 3755.4,229 3763.2,223.67 3768.1,214.84 \ +3771.2,206.08", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3909.4,178", + width=2.1304]; + "exposure event to outcome association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3976.9,221.5", + pos="e,3901.8,196.21 3041.5,251.78 3064.8,249.93 3088.8,248.23 3111.4,247 3153.6,244.71 3834.9,248.48 3872.4,229 3882.6,223.72 3890.7,\ +214.23 3896.7,204.93", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4098.4,178", + width=2.1304]; + "exposure event to outcome association" -> "object category closure" [color=blue, + label="object category closure", + lp="4166.9,221.5", + pos="e,4093.1,196.12 3040.9,251.73 3064.4,249.87 3088.6,248.18 3111.4,247 3137.9,245.62 4045.4,242.32 4068.4,229 4077.5,223.73 4084.2,\ +214.5 4088.8,205.4", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4288.4,178", + width=1.0652]; + "exposure event to outcome association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4338.4,221.5", + pos="e,4281.7,196.2 3040.4,251.72 3064,249.85 3088.4,248.16 3111.4,247 3143.1,245.4 4226.4,244.08 4254.4,229 4264.1,223.77 4271.6,214.42 \ +4277,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4447.4,178", + width=1.0652]; + "exposure event to outcome association" -> "object namespace" [color=blue, + label="object namespace", + lp="4491.4,221.5", + pos="e,4440,195.75 3040.4,251.68 3064,249.81 3088.4,248.13 3111.4,247 3147.4,245.22 4378.3,245.47 4410.4,229 4420.7,223.7 4428.9,214.02 \ +4434.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4598.4,178", + width=1.0652]; + "exposure event to outcome association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4651.4,221.5", + pos="e,4590.4,195.78 3040.1,251.68 3063.8,249.8 3088.3,248.12 3111.4,247 3151.6,245.05 4523.4,246.87 4559.4,229 4570.1,223.68 4578.8,\ +213.86 4585.2,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4769.4,178", + width=1.0652]; + "exposure event to outcome association" -> "object label closure" [color=blue, + label="object label closure", + lp="4817.9,221.5", + pos="e,4761.1,195.8 3039.9,251.67 3063.6,249.79 3088.2,248.11 3111.4,247 3156.3,244.85 4689,248.7 4729.4,229 4740.3,223.7 4749.1,213.89 \ +4755.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4931.4,178", + width=2.347]; + "exposure event to outcome association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4979.9,221.5", + pos="e,4922.8,196.3 3039.9,251.65 3063.6,249.77 3088.2,248.1 3111.4,247 3160.8,244.65 4846.9,250.64 4891.4,229 4902.1,223.78 4910.9,214.17 \ +4917.4,204.76", style=solid]; type [height=0.5, - pos="3349.4,178", + pos="5065.4,178", width=0.86659]; "exposure event to outcome association" -> type [color=blue, label=type, - lp="3379.4,221.5", - pos="e,3358.4,195.57 2022.4,251.69 2046,249.82 2070.4,248.14 2093.4,247 2110.9,246.13 3345.1,241.5 3357.4,229 3363.5,222.79 3363.7,213.89 \ -3361.6,205.31", + lp="5079.4,221.5", + pos="e,5066.2,196.19 3039.9,251.64 3063.6,249.76 3088.2,248.09 3111.4,247 3138.3,245.73 5032.3,245.8 5053.4,229 5060.2,223.55 5063.6,\ +214.93 5065.2,206.37", style=solid]; category [height=0.5, - pos="3450.4,178", + pos="5166.4,178", width=1.4263]; "exposure event to outcome association" -> category [color=blue, label=category, - lp="3453.9,221.5", - pos="e,3438.7,195.89 2022.4,251.68 2046,249.81 2070.4,248.13 2093.4,247 2129.6,245.21 3365.9,242.95 3399.4,229 3412.2,223.66 3423.6,213.41 \ -3432.3,203.58", + lp="5159.9,221.5", + pos="e,5150.8,195.26 3039.9,251.63 3063.6,249.76 3088.2,248.09 3111.4,247 3166.6,244.41 5047.1,246.64 5099.4,229 5115.6,223.54 5131.1,\ +212.51 5143.1,202.2", style=solid]; "population context qualifier" [color=blue, height=0.5, label="population of individual organisms", - pos="3691.4,178", + pos="5407.4,178", width=4.7662]; "exposure event to outcome association" -> "population context qualifier" [color=blue, label="population context qualifier", - lp="3667.4,221.5", - pos="e,3639.7,195.28 2022.1,251.68 2045.8,249.81 2070.3,248.13 2093.4,247 2248.3,239.43 3335.5,248.77 3489.4,229 3537.3,222.85 3590.2,\ -209.49 3629.9,198.12", + lp="5377.4,221.5", + pos="e,5353.5,195.22 3039.6,251.65 3063.4,249.76 3088.2,248.09 3111.4,247 3342.7,236.19 4965.5,256.75 5195.4,229 5246,222.9 5302,209.37 \ +5343.8,197.93", style=solid]; "temporal context qualifier" [color=blue, height=0.5, label="time type", - pos="3936.4,178", + pos="5652.4,178", width=1.5346]; "exposure event to outcome association" -> "temporal context qualifier" [color=blue, label="temporal context qualifier", - lp="3927.9,221.5", - pos="e,3902.4,192.33 2021.9,251.66 2045.6,249.79 2070.2,248.11 2093.4,247 2279.5,238.1 3586.2,257.15 3770.4,229 3812.9,222.51 3859.6,\ -207.71 3892.6,195.89", + lp="5640.9,221.5", + pos="e,5617.8,192.13 3039.6,251.63 3063.4,249.74 3088.2,248.07 3111.4,247 3242.9,240.92 5350.2,248.05 5480.4,229 5524.8,222.51 5573.8,\ +207.45 5608.1,195.55", style=solid]; subject -> object [label=relation, lp="1289.4,134.5", @@ -269,11 +385,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2140.4,265", + pos="3158.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2271.4,265", + pos="3289.4,265", width=2.0762]; } diff --git a/graphviz/exposure_event_to_outcome_association.svg b/graphviz/exposure_event_to_outcome_association.svg index c3290f9a1e..c431af7d59 100644 --- a/graphviz/exposure_event_to_outcome_association.svg +++ b/graphviz/exposure_event_to_outcome_association.svg @@ -4,16 +4,16 @@ - + %3 - + exposure event to outcome association - -exposure event to outcome association + +exposure event to outcome association @@ -24,9 +24,9 @@ exposure event to outcome association->association - - -is_a + + +is_a @@ -37,8 +37,8 @@ exposure event to outcome association->entity to outcome association mixin - - + + uses @@ -50,9 +50,9 @@ exposure event to outcome association->id - - -id + + +id @@ -63,9 +63,9 @@ exposure event to outcome association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ exposure event to outcome association->name - - -name + + +name @@ -89,9 +89,9 @@ exposure event to outcome association->description - - -description + + +description @@ -102,9 +102,9 @@ exposure event to outcome association->has attribute - - -has attribute + + +has attribute @@ -115,8 +115,8 @@ exposure event to outcome association->subject - - + + subject @@ -128,8 +128,8 @@ exposure event to outcome association->predicate - - + + predicate @@ -141,7 +141,7 @@ exposure event to outcome association->object - + object @@ -154,9 +154,9 @@ exposure event to outcome association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ exposure event to outcome association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ exposure event to outcome association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ exposure event to outcome association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ exposure event to outcome association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ exposure event to outcome association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ exposure event to outcome association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ exposure event to outcome association->timepoint - - -timepoint + + +timepoint @@ -258,9 +258,9 @@ exposure event to outcome association->original subject - - -original subject + + +original subject @@ -271,111 +271,254 @@ exposure event to outcome association->original predicate - - -original predicate + + +original predicate original object - -string + +string exposure event to outcome association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +exposure event to outcome association->subject category + + +subject category + + + +object category + +ontology class + + + +exposure event to outcome association->object category + + +object category + + + +subject closure + +string + + + +exposure event to outcome association->subject closure + + +subject closure + + + +object closure + +string + + + +exposure event to outcome association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +exposure event to outcome association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +exposure event to outcome association->object category closure + + +object category closure + + + +subject namespace + +string + + + +exposure event to outcome association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +exposure event to outcome association->object namespace + + +object namespace + + + +subject label closure + +string + + + +exposure event to outcome association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +exposure event to outcome association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +exposure event to outcome association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + exposure event to outcome association->type - - -type + + +type - + category - -category + +category - + exposure event to outcome association->category - - -category + + +category - + population context qualifier - -population of individual organisms + +population of individual organisms - + exposure event to outcome association->population context qualifier - - -population context qualifier + + +population context qualifier - + temporal context qualifier - -time type + +time type - + exposure event to outcome association->temporal context qualifier - - -temporal context qualifier + + +temporal context qualifier - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/exposure_event_to_phenotypic_feature_association.gv b/graphviz/exposure_event_to_phenotypic_feature_association.gv index ad058dcd62..59958e173d 100644 --- a/graphviz/exposure_event_to_phenotypic_feature_association.gv +++ b/graphviz/exposure_event_to_phenotypic_feature_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,4596.4,283"]; + graph [bb="0,0,6258.4,283"]; node [label="\N"]; "exposure event to phenotypic feature association" [height=0.5, label="exposure event to phenotypic feature association", - pos="2576.4,265", + pos="3379.4,265", width=6.6439]; association [height=0.5, pos="62.394,178", width=1.7332]; "exposure event to phenotypic feature association" -> association [label=is_a, - lp="580.39,221.5", - pos="e,107.12,190.7 2337.2,264.38 1960.4,263.96 1205.7,258.96 566.39,229 374.05,219.99 324.67,225.55 134.39,196 128.7,195.12 122.8,194.02 \ -116.92,192.81"]; + lp="570.39,221.5", + pos="e,107.12,190.68 3141.5,263.06 2556,260.43 1056.5,251.63 556.39,229 368.46,220.5 320.27,225.03 134.39,196 128.7,195.11 122.8,194.01 \ +116.93,192.8"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "exposure event to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="743.89,221.5", - pos="e,457.32,194.52 2338.4,263.03 1911.9,260.69 1033.1,253.03 727.39,229 639.08,222.06 539.35,207.69 467.3,196.13"]; + pos="e,456.57,194.54 3140.2,264.67 2579.4,265.62 1192,264.19 727.39,229 638.76,222.29 538.66,207.82 466.55,196.17"]; id [color=blue, height=0.5, label=string, @@ -26,8 +26,8 @@ digraph { "exposure event to phenotypic feature association" -> id [color=blue, label=id, lp="861.39,221.5", - pos="e,677.38,189.97 2337.2,264.62 1933.6,264.74 1134,260.77 854.39,229 783.12,220.9 765.47,215.35 696.39,196 693.29,195.13 690.09,194.16 \ -686.89,193.14", + pos="e,677.38,189.97 3141.3,263.31 2555.8,261.23 1077.2,253.58 854.39,229 783.09,221.13 765.47,215.35 696.39,196 693.29,195.13 690.09,\ +194.16 686.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -37,7 +37,7 @@ digraph { "exposure event to phenotypic feature association" -> iri [color=blue, label=iri, lp="958.39,221.5", - pos="e,782.71,189.98 2337,264.66 1951.8,264.73 1211.2,260.56 950.39,229 894.94,222.29 832.78,205.31 792.47,193", + pos="e,782.7,190.05 3141.2,263.34 2571.8,261.38 1163.4,254.02 950.39,229 894.92,222.49 832.76,205.47 792.46,193.09", style=solid]; name [color=blue, height=0.5, @@ -47,7 +47,7 @@ digraph { "exposure event to phenotypic feature association" -> name [color=blue, label=name, lp="1054.4,221.5", - pos="e,902.73,192.32 2340.1,262.14 1939.8,258.47 1159.3,248.85 1034.4,229 992.1,222.28 945.54,207.58 912.52,195.85", + pos="e,902.72,192.4 3140.4,264.19 2584.7,264.09 1237.9,260.54 1034.4,229 992.08,222.44 945.52,207.73 912.51,195.95", style=solid]; description [color=blue, height=0.5, @@ -57,7 +57,7 @@ digraph { "exposure event to phenotypic feature association" -> description [color=blue, label=description, lp="1157.9,221.5", - pos="e,1042.8,195.22 2337.5,264.02 1954,263.19 1232,257.75 1117.4,229 1094.1,223.16 1070,211.16 1051.5,200.38", + pos="e,1042.8,195.28 3141.4,263.19 2580.2,260.88 1214.2,252.85 1117.4,229 1094.1,223.26 1070,211.26 1051.5,200.46", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,7 +67,7 @@ digraph { "exposure event to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1277.4,221.5", - pos="e,1179.3,195.41 2341.4,261.58 1969.5,257.21 1281.8,246.8 1230.4,229 1214.3,223.44 1199,212.52 1187,202.3", + pos="e,1179,195.22 3140.5,264.04 2599.3,263.6 1319.3,259.33 1230.4,229 1214.2,223.48 1198.7,212.45 1186.7,202.15", style=solid]; predicate [color=blue, height=0.5, @@ -77,18 +77,18 @@ digraph { "exposure event to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1377.4,221.5", - pos="e,1317.4,196.12 2338.6,262.94 1992.4,260.58 1385.8,253.02 1343.4,229 1334,223.67 1326.9,214.3 1321.8,205.1", + pos="e,1317.4,196.16 3141.7,262.84 2612.9,259.86 1382.1,250.63 1343.4,229 1333.9,223.72 1326.9,214.36 1321.8,205.16", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="3387.4,91", + pos="5049.4,91", width=1.9318]; "exposure event to phenotypic feature association" -> object [color=blue, label=object, lp="1456.4,178", - pos="e,3317.7,91.747 2339.5,262.46 2152.1,259.46 1884,251.19 1650.4,229 1550.1,219.47 1364.4,232.49 1434.4,160 1500.5,91.603 2949,90.853 \ -3307.6,91.721", + pos="e,4979.7,91.969 3141.2,263.07 2736.7,260.85 1931.6,253.4 1649.4,229 1549.4,220.35 1364.1,231.63 1434.4,160 1498.5,94.718 4444.1,\ +91.943 4969.6,91.968", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "exposure event to phenotypic feature association" -> negated [color=blue, label=negated, - lp="1759.4,221.5", - pos="e,1569,190.38 2349,259.42 2139.8,254.32 1845.3,244.68 1730.4,229 1677.3,221.76 1617.9,205.39 1578.5,193.34", + lp="1757.4,221.5", + pos="e,1568.2,190.48 3143.7,261.77 2720.9,257.36 1864.5,246.4 1728.4,229 1675.8,222.28 1617.1,205.84 1578.2,193.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "exposure event to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="1891.9,221.5", - pos="e,1717,193.16 2353.5,258.43 2178.8,253.08 1950.3,243.61 1858.4,229 1813.2,221.81 1763.2,207.7 1726.8,196.3", + lp="1896.9,221.5", + pos="e,1717.4,193.23 3144.4,261.63 2750.1,257.2 1986.2,246.5 1863.4,229 1816.4,222.31 1764.4,207.91 1727,196.28", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "exposure event to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2027.4,221.5", - pos="e,1866.5,193.14 2361,257.16 2221.7,251.6 2053.6,242.46 1983.4,229 1946.4,221.9 1905.9,208.15 1876.1,196.86", + lp="2042.4,221.5", + pos="e,1868.3,192.88 3144.5,261.46 2779.9,257.01 2107.9,246.55 1998.4,229 1956.8,222.33 1911,208 1878.1,196.38", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,8 +127,8 @@ digraph { width=2.0943]; "exposure event to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2170.9,221.5", - pos="e,2021.7,194.19 2351.6,258.79 2278.5,253.87 2197.4,244.94 2124.4,229 2092.2,221.98 2057.4,209.06 2031,198.12", + lp="2201.9,221.5", + pos="e,2026.5,193.55 3140.3,264.58 2838.9,264.03 2338.2,258.45 2155.4,229 2114.4,222.39 2069.3,208.49 2036.4,197.02", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -137,8 +137,8 @@ digraph { width=3.015]; "exposure event to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2306.9,221.5", - pos="e,2203,195.94 2383.1,254.38 2324.4,249.16 2268.6,241.16 2242.4,229 2230,223.23 2218.7,213.26 2209.8,203.74", + lp="2357.9,221.5", + pos="e,2216.8,195.64 3144.2,261.62 2849.5,257.84 2373.3,248.74 2293.4,229 2269.6,223.12 2244.8,211.28 2225.5,200.6", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -147,8 +147,8 @@ digraph { width=3.015]; "exposure event to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2473.4,221.5", - pos="e,2394.2,195.46 2429.6,250.78 2405.9,245.71 2386.5,238.7 2378.4,229 2370.6,219.76 2376.4,210.01 2386.1,201.6", + lp="2529.4,221.5", + pos="e,2423.5,196.48 3142.1,262.57 2870.9,259.84 2460.8,251.93 2434.4,229 2428,223.41 2425.1,214.91 2424,206.5", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -157,8 +157,8 @@ digraph { width=3.015]; "exposure event to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2683.9,221.5", - pos="e,2602.3,193.23 2572.3,246.85 2570.9,236.48 2571,223.49 2577.4,214 2581.6,207.77 2587.2,202.65 2593.4,198.43", + lp="2738.9,221.5", + pos="e,2640.7,196.14 3146.9,260.78 2934.3,256.66 2650.2,247.68 2632.4,229 2625.5,221.8 2628.3,212.59 2634.2,204.05", style=solid]; timepoint [color=blue, height=0.5, @@ -167,8 +167,8 @@ digraph { width=1.5346]; "exposure event to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="2846.4,221.5", - pos="e,2829.7,195.66 2727.7,251.04 2749.4,245.85 2771,238.73 2790.4,229 2802.6,222.87 2813.9,212.85 2822.8,203.39", + lp="2895.4,221.5", + pos="e,2843.9,196.19 3149.5,259.98 3021.9,255.73 2884.2,246.98 2860.4,229 2853.1,223.49 2848.7,214.74 2846.2,206.1", style=solid]; "original subject" [color=blue, height=0.5, @@ -177,8 +177,8 @@ digraph { width=1.0652]; "exposure event to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="2961.4,221.5", - pos="e,2934.2,193.57 2744.6,252.17 2801.5,246.59 2857.3,238.94 2883.4,229 2885.9,228.05 2907.3,212.91 2925.9,199.53", + lp="2994.4,221.5", + pos="e,2941.9,195.19 3152.7,259.25 3052.7,254.75 2954.1,246 2938.4,229 2932.1,222.22 2933.3,212.97 2937.1,204.27", style=solid]; "original predicate" [color=blue, height=0.5, @@ -187,8 +187,8 @@ digraph { width=1.5887]; "exposure event to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3102.9,221.5", - pos="e,3056.5,196.06 2743.5,252.09 2866,243.16 3011.9,231.97 3018.4,229 3030.6,223.38 3041.5,213.43 3050,203.88", + lp="3121.9,221.5", + pos="e,3058.6,195.75 3192.2,253.77 3127.5,248.29 3068.5,240.29 3058.4,229 3052.6,222.56 3052.7,213.75 3055,205.31", style=solid]; "original object" [color=blue, height=0.5, @@ -197,148 +197,263 @@ digraph { width=1.0652]; "exposure event to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3230.9,221.5", - pos="e,3182.4,196.12 2744.5,252.16 2771.5,250.36 2799.2,248.58 2825.4,247 2863.5,244.7 3138.6,252.85 3168.4,229 3175.3,223.47 3179,214.84 \ -3180.9,206.29", + lp="3250.9,221.5", + pos="e,3183.9,196.25 3257.1,249.46 3231.5,244.34 3209.3,237.63 3199.4,229 3192.7,223.17 3188.7,214.61 3186.2,206.22", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3315.4,178", + width=2.1304]; + "exposure event to phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3368.9,221.5", + pos="e,3308.1,196.39 3328.7,247.39 3321,242.65 3314.1,236.63 3309.4,229 3305.2,222.28 3304.8,214.07 3305.9,206.26", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3486.4,178", + width=2.1304]; + "exposure event to phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3501.9,221.5", + pos="e,3468,195.66 3404.1,246.98 3412,241.4 3420.7,235.07 3428.4,229 3439.1,220.58 3450.6,210.87 3460.4,202.27", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3619.4,178", + width=1.0652]; + "exposure event to phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="3638.9,221.5", + pos="e,3605.2,195.02 3502.2,249.49 3522.5,244.54 3543,237.9 3561.4,229 3574.9,222.45 3587.8,211.92 3598,202.21", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3715.4,178", + width=1.0652]; + "exposure event to phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="3756.4,221.5", + pos="e,3712.8,196.12 3550.2,252.39 3617.4,246.43 3681.8,238.43 3694.4,229 3702,223.35 3706.8,214.45 3709.9,205.72", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3848.4,178", + width=2.1304]; + "exposure event to phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3914.9,221.5", + pos="e,3840.3,195.98 3545.8,252.03 3664.6,243.25 3804.4,232.3 3810.4,229 3820.5,223.44 3828.8,213.91 3835,204.64", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4037.4,178", + width=2.1304]; + "exposure event to phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4104.9,221.5", + pos="e,4031.7,196.03 3546.8,252.1 3574.1,250.29 3602,248.53 3628.4,247 3670.4,244.57 3970.2,250.32 4006.4,229 4015.5,223.62 4022.4,214.37 \ +4027.3,205.28", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4227.4,178", + width=1.0652]; + "exposure event to phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4277.4,221.5", + pos="e,4220.4,196.15 3544.1,251.91 3572.2,250.09 3601.1,248.37 3628.4,247 3659.7,245.43 4164.8,243.92 4192.4,229 4202.2,223.71 4209.8,\ +214.34 4215.4,205.14", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4386.4,178", + width=1.0652]; + "exposure event to phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4430.4,221.5", + pos="e,4379,195.71 3542.7,251.83 3571.3,250 3600.7,248.29 3628.4,247 3668.4,245.13 4313.8,247.48 4349.4,229 4359.7,223.64 4367.9,213.95 \ +4373.9,204.52", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4537.4,178", + width=1.0652]; + "exposure event to phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4590.4,221.5", + pos="e,4529.4,195.75 3542.1,251.78 3570.8,249.94 3600.5,248.24 3628.4,247 3676.7,244.85 4455.2,250.66 4498.4,229 4509.1,223.64 4517.7,\ +213.81 4524.1,204.28", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4657.4,178", + width=1.0652]; + "exposure event to phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="4743.9,221.5", + pos="e,4667.7,195.5 3541.4,251.74 3570.4,249.89 3600.3,248.2 3628.4,247 3657.3,245.77 4648.1,249.61 4668.4,229 4674.6,222.64 4674.3,213.6 \ +4671.6,204.94", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4798.4,178", + width=2.347]; + "exposure event to phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4891.9,221.5", + pos="e,4813.2,196.2 3541.1,251.71 3570.1,249.86 3600.1,248.18 3628.4,247 3661.4,245.62 4794.2,252.53 4817.4,229 4823.9,222.42 4822.5,\ +213.41 4818.3,204.84", style=solid]; type [height=0.5, - pos="3270.4,178", + pos="4932.4,178", width=0.86659]; "exposure event to phenotypic feature association" -> type [color=blue, label=type, - lp="3307.4,221.5", - pos="e,3282.7,194.83 2742.1,252.01 2769.9,250.19 2798.5,248.44 2825.4,247 2851,245.63 3268.6,247.47 3286.4,229 3293,222.17 3291.6,212.65 \ -3287.6,203.75", + lp="4986.4,221.5", + pos="e,4951.1,192.56 3540.7,251.69 3569.9,249.84 3600,248.16 3628.4,247 3647,246.24 4952.4,242.22 4965.4,229 4974,220.33 4967.8,209.12 \ +4958.5,199.52", style=solid]; category [height=0.5, - pos="3371.4,178", + pos="5033.4,178", width=1.4263]; "exposure event to phenotypic feature association" -> category [color=blue, label=category, - lp="3377.9,221.5", - pos="e,3361.8,195.73 2741.8,251.96 2769.7,250.14 2798.3,248.41 2825.4,247 2881.1,244.1 3277,252.9 3327.4,229 3338.9,223.56 3348.6,213.59 \ -3356,203.97", + lp="5051.9,221.5", + pos="e,5029.1,196.09 3540.7,251.68 3569.9,249.83 3600,248.15 3628.4,247 3666.6,245.45 4973.6,248.82 5006.4,229 5015.1,223.75 5021.1,214.65 \ +5025.3,205.64", style=solid]; subject [height=0.5, - pos="3485.4,178", + pos="5147.4,178", width=1.2277]; "exposure event to phenotypic feature association" -> subject [color=blue, label=subject, - lp="3469.4,221.5", - pos="e,3468.6,194.9 2740.8,251.9 2769,250.08 2798,248.35 2825.4,247 2890.7,243.77 3351.3,249.49 3413.4,229 3430.7,223.29 3447.6,211.98 \ -3460.6,201.56", + lp="5139.4,221.5", + pos="e,5133.5,195.46 3540.4,251.69 3569.7,249.83 3599.9,248.15 3628.4,247 3668.9,245.37 5049.4,243.03 5087.4,229 5102.1,223.56 5115.8,\ +212.8 5126.4,202.65", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3632.4,178", + pos="5294.4,178", width=2.3651]; "exposure event to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3620.4,221.5", - pos="e,3599.9,194.69 2740.1,251.85 2768.5,250.02 2797.8,248.31 2825.4,247 2975.1,239.9 3352.3,257.76 3499.4,229 3531,222.83 3564.9,209.98 \ -3590.5,198.85", + lp="5287.4,221.5", + pos="e,5264,194.83 3540.4,251.67 3569.7,249.81 3599.9,248.14 3628.4,247 3713.9,243.58 5085.4,245.68 5169.4,229 5199.1,223.09 5230.9,210.32 \ +5254.9,199.17", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="3811.4,178", + pos="5473.4,178", width=2.1123]; "exposure event to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="3801.4,221.5", - pos="e,3782.6,194.75 2739.1,251.78 2767.8,249.94 2797.5,248.24 2825.4,247 2921.7,242.72 3598.1,249.02 3692.4,229 3720.7,222.99 3750.8,\ -210.31 3773.6,199.22", + lp="5466.4,221.5", + pos="e,5445.9,194.84 3540.1,251.66 3569.4,249.8 3599.8,248.12 3628.4,247 3724.5,243.22 5265.4,249.22 5359.4,229 5386.6,223.15 5415.2,\ +210.56 5437,199.48", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="3941.4,178", + pos="5603.4,178", width=1.011]; "exposure event to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="3948.9,221.5", - pos="e,3924.7,194.26 2738.4,251.74 2767.4,249.89 2797.3,248.2 2825.4,247 2883.2,244.53 3811.2,246.24 3866.4,229 3884.8,223.24 3902.9,\ -211.42 3916.7,200.72", + lp="5612.9,221.5", + pos="e,5587.5,194.3 3540.1,251.64 3569.4,249.78 3599.8,248.11 3628.4,247 3681.2,244.95 5481,245.04 5531.4,229 5549.3,223.3 5566.7,211.48 \ +5579.9,200.76", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="4069.4,178", + pos="5731.4,178", width=2.0401]; "exposure event to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="4076.4,221.5", - pos="e,4053.8,195.71 2738.1,251.71 2767.1,249.86 2797.1,248.18 2825.4,247 2890.8,244.27 3942.5,250.57 4004.4,229 4020,223.55 4034.8,212.75 \ -4046.4,202.58", + lp="5739.4,221.5", + pos="e,5716.2,195.98 3540.1,251.63 3569.4,249.76 3599.8,248.1 3628.4,247 3685,244.82 5615,247.89 5668.4,229 5683.4,223.68 5697.6,213.15 \ +5708.7,203.12", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="4205.4,178", + pos="5867.4,178", width=1.2277]; "exposure event to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="4193.4,221.5", - pos="e,4186.8,194.54 2737.7,251.7 2766.9,249.84 2797,248.16 2825.4,247 2897.5,244.04 4055.1,249.18 4124.4,229 4144,223.28 4163.6,211.41 \ -4178.6,200.67", + lp="5855.4,221.5", + pos="e,5849.1,194.57 3539.7,251.64 3569.2,249.77 3599.7,248.1 3628.4,247 3688.3,244.71 5729.8,245.77 5787.4,229 5806.8,223.33 5826.2,\ +211.47 5841,200.71", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="4311.4,178", + pos="5973.4,178", width=1.2277]; "exposure event to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="4296.9,221.5", - pos="e,4293.4,194.54 2737.7,251.68 2766.9,249.82 2797,248.15 2825.4,247 2903.5,243.84 4157.5,251.24 4232.4,229 4251.6,223.29 4270.7,211.42 \ -4285.3,200.68", + lp="5958.9,221.5", + pos="e,5955.4,194.57 3539.7,251.63 3569.2,249.76 3599.7,248.09 3628.4,247 3691.3,244.61 5834,246.76 5894.4,229 5913.7,223.33 5932.8,211.47 \ +5947.3,200.71", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="4415.4,178", + pos="6077.4,178", width=1.1735]; "exposure event to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="4411.4,221.5", - pos="e,4396.7,194.31 2737.4,251.68 2766.7,249.82 2796.9,248.14 2825.4,247 2909.1,243.65 4251.9,251.9 4332.4,229 4352.5,223.27 4372.7,\ -211.28 4388.2,200.48", + lp="6073.4,221.5", + pos="e,6058.7,194.34 3539.7,251.62 3569.2,249.75 3599.7,248.09 3628.4,247 3694.1,244.51 5931.1,246.84 5994.4,229 6014.6,223.31 6034.8,\ +211.32 6050.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4522.4,178", + pos="6184.4,178", width=1.1735]; "exposure event to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="4541.4,221.5", - pos="e,4507.9,195.47 2737.4,251.66 2766.7,249.8 2796.9,248.13 2825.4,247 2870.8,245.2 4417.6,244.35 4460.4,229 4475.5,223.58 4489.6,212.83 \ -4500.6,202.67", + lp="6203.4,221.5", + pos="e,6170.4,195 3539.7,251.61 3569.2,249.74 3599.7,248.08 3628.4,247 3697.6,244.39 6057.1,252.3 6122.4,229 6137.7,223.54 6152,212.56 \ +6163,202.28", style=solid]; relation [height=0.5, - pos="3436.4,18", + pos="5098.4,18", width=1.2999]; - object -> relation [pos="e,3424.9,35.705 3399,73.174 3405,64.509 3412.4,53.768 3419,44.141", + object -> relation [pos="e,5086.9,35.705 5061,73.174 5067,64.509 5074.4,53.768 5081,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="2872.4,265", + pos="3675.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3003.4,265", + pos="3806.4,265", width=2.0762]; subject -> object [label=relation, - lp="3443.4,134.5", - pos="e,3393.8,108.97 3452.9,165.59 3440.1,159.94 3426,152.13 3415.4,142 3408.4,135.31 3402.7,126.48 3398.3,118.1"]; - subject -> relation [pos="e,3447.6,35.828 3484,159.99 3481.9,139.02 3477,102.55 3466.4,73 3462.9,63.258 3457.8,53.189 3452.8,44.423", + lp="5105.4,134.5", + pos="e,5055.8,108.97 5114.9,165.59 5102.1,159.94 5088,152.13 5077.4,142 5070.4,135.31 5064.7,126.48 5060.3,118.1"]; + subject -> relation [pos="e,5109.6,35.828 5146,159.99 5143.9,139.02 5139,102.55 5128.4,73 5124.9,63.258 5119.8,53.189 5114.8,44.423", style=dotted]; "exposure event to phenotypic feature association_subject" [color=blue, height=0.5, label="exposure event", - pos="3178.4,265", + pos="3981.4,265", width=2.2748]; } diff --git a/graphviz/exposure_event_to_phenotypic_feature_association.svg b/graphviz/exposure_event_to_phenotypic_feature_association.svg index 19e96ad307..93c8dd99a3 100644 --- a/graphviz/exposure_event_to_phenotypic_feature_association.svg +++ b/graphviz/exposure_event_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + exposure event to phenotypic feature association - -exposure event to phenotypic feature association + +exposure event to phenotypic feature association @@ -24,9 +24,9 @@ exposure event to phenotypic feature association->association - - -is_a + + +is_a @@ -37,8 +37,8 @@ exposure event to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,7 +50,7 @@ exposure event to phenotypic feature association->id - + id @@ -63,8 +63,8 @@ exposure event to phenotypic feature association->iri - - + + iri @@ -76,8 +76,8 @@ exposure event to phenotypic feature association->name - - + + name @@ -89,8 +89,8 @@ exposure event to phenotypic feature association->description - - + + description @@ -102,8 +102,8 @@ exposure event to phenotypic feature association->has attribute - - + + has attribute @@ -115,21 +115,21 @@ exposure event to phenotypic feature association->predicate - - + + predicate object - -named thing + +named thing exposure event to phenotypic feature association->object - - + + object @@ -141,9 +141,9 @@ exposure event to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ exposure event to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ exposure event to phenotypic feature association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ exposure event to phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ exposure event to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ exposure event to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ exposure event to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ exposure event to phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ exposure event to phenotypic feature association->original subject - - -original subject + + +original subject @@ -258,9 +258,9 @@ exposure event to phenotypic feature association->original predicate - - -original predicate + + +original predicate @@ -271,195 +271,338 @@ exposure event to phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +exposure event to phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +exposure event to phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +exposure event to phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +exposure event to phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +exposure event to phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +exposure event to phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +exposure event to phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +exposure event to phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +exposure event to phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +exposure event to phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +exposure event to phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + exposure event to phenotypic feature association->type - - -type + + +type - + category - -category + +category - + exposure event to phenotypic feature association->category - - -category + + +category - + subject - -subject + +subject - + exposure event to phenotypic feature association->subject - - -subject + + +subject - + frequency qualifier - -frequency value + +frequency value - + exposure event to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + exposure event to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + exposure event to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier - + sex qualifier - -biological sex + +biological sex - + exposure event to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier - + has count - -integer + +integer - + exposure event to phenotypic feature association->has count - - -has count + + +has count - + has total - -integer + +integer - + exposure event to phenotypic feature association->has total - - -has total + + +has total - + has quotient - -double + +double - + exposure event to phenotypic feature association->has quotient - - -has quotient + + +has quotient - + has percentage - -double + +double - + exposure event to phenotypic feature association->has percentage - - -has percentage + + +has percentage - + relation - -relation + +relation - + object->relation - - + + - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + subject->relation - - + + - + exposure event to phenotypic feature association_subject - -exposure event + +exposure event diff --git a/graphviz/functional_association.gv b/graphviz/functional_association.gv index 9a10a92dd2..69f594afaa 100644 --- a/graphviz/functional_association.gv +++ b/graphviz/functional_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "functional association" [height=0.5, label="functional association", - pos="1542.4,265", + pos="2492.4,265", width=3.1053]; association [height=0.5, pos="62.394,178", width=1.7332]; "functional association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1430.4,263.93 1162.8,263.27 491.98,258.61 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2380.6,263.71 1958.9,262.4 477.37,255.91 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "functional association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1431.2,262.94 1183.9,260.19 594.43,251.44 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,\ -194.16 219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2381,263.35 1975.2,260.8 589.15,250.6 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "functional association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1431.7,262.22 1204.8,258.24 693.35,247.48 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,\ -194.19 324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2381.2,263.16 1990.3,260.04 693.38,248.34 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ +194.18 325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "functional association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1431.8,262.32 1221.4,258.7 770.87,248.86 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2380.9,263.31 2002.7,260.79 782.66,251.03 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "functional association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1431.2,262.61 1239.5,259.64 854.57,251.08 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2380.6,263.59 2016.6,262.01 878.85,255.01 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "functional association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1432.7,261.38 1270.2,256.97 973.6,246.78 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2380.9,263.31 2038.3,260.94 1014.7,251.99 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "functional association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1431.7,262.37 1328.3,259.43 1170,251.32 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2380.5,264.56 2086.8,265.52 1298.6,264.58 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "functional association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1438.2,258.45 1363.7,253.43 1261.4,244.41 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2380.5,263.73 2108.8,262.65 1419.9,257.11 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "functional association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1449.1,255 1400.5,249.36 1340.4,240.88 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2380.7,263.8 2129.4,262.84 1525.2,257.53 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "functional association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1473.8,250.75 1448.5,245.09 1419.9,237.76 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2380.5,263.78 2150.2,262.75 1630.6,257.25 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "functional association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461,195.47 1522.4,247.21 1507.1,234.32 1485.8,216.38 1468.9,202.13", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2380.9,263.13 2177.1,260.95 1752,253.53 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "functional association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1569.9,247.49 1578.4,241.98 1587.5,235.56 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2380.5,264.75 2200.7,264.96 1856,260.97 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "functional association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1626.2,253.05 1662.8,247.35 1706.1,239.37 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2382.4,261.61 2210.1,257.32 1894.4,247.04 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "functional association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2080.1,195.14 1620.4,252.07 1634.7,250.16 1649.5,248.37 1663.4,247 1805.2,233.08 1844.1,258.93 1983.4,229 2013.6,222.51 2046,210.06 \ -2070.9,199.2", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2381.8,262.33 2265,259.38 2094.9,251.28 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "functional association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.78 1619.4,251.9 1634,249.98 1649.1,248.22 1663.4,247 1728.2,241.47 2189.1,255.73 2248.4,229 2260.4,223.57 2270.9,213.45 \ -2278.8,203.74", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2391.1,257.32 2350.5,252.38 2310.3,243.82 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "functional association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.23 1619.1,251.9 1633.7,249.96 1649,248.2 1663.4,247 1738.6,240.74 2271.3,254.25 2342.4,229 2351.2,225.87 2368.2,212.74 \ -2382.5,200.72", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2407.2,253.21 2394.4,247.87 2382.7,240.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,203 @@ digraph { width=1.5887]; "functional association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.25 1619.1,251.84 1633.7,249.91 1649,248.16 1663.4,247 1708.7,243.33 2440.6,249.14 2481.4,229 2492.1,223.72 2500.8,214.1 \ -2507.4,204.69", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "functional association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.99 1618.7,251.85 1633.5,249.9 1648.9,248.15 1663.4,247 1690.2,244.88 2607.9,243.7 2630.4,229 2638.5,223.68 2643.8,214.69 \ -2647.3,205.8", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2578.3,253.37 2593.8,248.09 2608.8,240.34 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "functional association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2573.6,252.6 2644.6,242.61 2736.5,229.58 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "functional association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.7,195.65 2571.1,252.12 2585.1,250.23 2599.7,248.43 2613.4,247 2671.4,240.94 2820.9,249.88 2875.4,229 2890.4,223.24 2904.8,\ +212.66 2916.1,202.71", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "functional association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.27 2570.1,251.98 2584.4,250.07 2599.3,248.3 2613.4,247 2658,242.88 2974.9,245.91 3016.4,229 3030.2,223.36 3042.9,212.73 \ +3052.7,202.72", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "functional association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.35 2569.4,251.93 2584,250 2599.1,248.24 2613.4,247 2643.2,244.41 3127.9,246.21 3152.4,229 3160.1,223.62 3164.8,214.78 \ +3167.7,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "functional association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.19 2569.4,251.87 2584,249.94 2599.1,248.19 2613.4,247 2649.7,243.96 3236.1,245.83 3268.4,229 3278.6,223.7 3286.6,214.21 \ +3292.6,204.91", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "functional association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.16 2569.1,251.83 2583.7,249.9 2599,248.16 2613.4,247 2660.5,243.2 3423,251.85 3464.4,229 3474,223.72 3481.2,214.36 \ +3486.5,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "functional association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.73 2568.7,251.83 2583.5,249.89 2598.9,248.14 2613.4,247 2670.9,242.48 3600.3,255.74 3651.4,229 3661.6,223.66 3669.6,\ +213.98 3675.4,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "functional association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.76 2568.7,251.81 2583.5,249.86 2598.9,248.12 2613.4,247 2646.5,244.44 3778.8,243.98 3808.4,229 3818.9,223.71 3827.2,\ +214.03 3833.4,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "functional association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.78 2568.7,251.79 2583.5,249.84 2598.9,248.11 2613.4,247 2650.6,244.15 3924.9,245.62 3958.4,229 3969.1,223.68 3977.8,\ +213.86 3984.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "functional association" -> "object label closure" [color=blue, + label="object label closure", + lp="4216.9,221.5", + pos="e,4160.1,195.8 2568.7,251.77 2583.5,249.83 2598.9,248.1 2613.4,247 2655.4,243.82 4090.6,247.46 4128.4,229 4139.3,223.7 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "functional association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.8,196.3 2568.4,251.8 2583.3,249.84 2598.8,248.1 2613.4,247 2659.8,243.5 4248.5,249.41 4290.4,229 4301.1,223.78 4309.9,214.17 \ +4316.4,204.75", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "functional association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.55 1618.7,251.82 1633.5,249.88 1648.9,248.13 1663.4,247 1693.5,244.64 2729.2,250.53 2750.4,229 2756.6,222.7 2756.6,\ -213.66 2754.2,205", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2568.4,251.79 2583.3,249.83 2598.8,248.09 2613.4,247 2638.9,245.09 4432.4,244.91 4452.4,229 4459.2,223.54 4462.6,\ +214.93 4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "functional association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.87 1618.7,251.82 1633.5,249.87 1648.9,248.13 1663.4,247 1725.9,242.13 2734.6,253.47 2792.4,229 2804.9,223.69 2816,213.59 \ -2824.5,203.85", + lp="4558.9,221.5", + pos="e,4549.8,195.26 2568.4,251.78 2583.3,249.83 2598.8,248.09 2613.4,247 2665.6,243.1 4448.8,245.74 4498.4,229 4514.6,223.53 4530.1,\ +212.51 4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "functional association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.76 1618.7,251.8 1633.5,249.86 1648.9,248.12 1663.4,247 1730.9,241.78 2817.8,249.31 2882.4,229 2900.4,223.34 2918,211.76 \ -2931.5,201.16", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2568.4,251.78 2583.3,249.82 2598.8,248.09 2613.4,247 2723.2,238.83 4488.3,258.4 4594.4,229 4615.1,223.25 4636,211.09 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "functional association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1618.7,251.79 1633.5,249.85 1648.9,248.11 1663.4,247 1735.7,241.44 2901.3,254 2969.4,229 3011.9,213.4 3017.1,186.96 \ -3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2568.4,251.77 2583.3,249.82 2598.8,248.08 2613.4,247 2670.8,242.74 4630.6,246.58 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1710.4,265", + pos="2660.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1841.4,265", + pos="2791.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="2090.4,265", + pos="3040.4,265", width=4.3329]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "functional association_object" [color=blue, height=0.5, label="ontology class", - pos="2341.4,265", + pos="3291.4,265", width=2.1304]; } diff --git a/graphviz/functional_association.svg b/graphviz/functional_association.svg index aaf26a6a5a..9dfe113a46 100644 --- a/graphviz/functional_association.svg +++ b/graphviz/functional_association.svg @@ -4,16 +4,16 @@ - + %3 - + functional association - -functional association + +functional association @@ -24,9 +24,9 @@ functional association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ functional association->id - - -id + + +id @@ -50,9 +50,9 @@ functional association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ functional association->name - - -name + + +name @@ -76,9 +76,9 @@ functional association->description - - -description + + +description @@ -89,9 +89,9 @@ functional association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ functional association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ functional association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ functional association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ functional association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ functional association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ functional association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ functional association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ functional association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ functional association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ functional association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ functional association->original predicate - - -original predicate + + +original predicate original object - -string + +string functional association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +functional association->subject category + + +subject category + + + +object category + +ontology class + + + +functional association->object category + + +object category + + + +subject closure + +string + + + +functional association->subject closure + + +subject closure + + + +object closure + +string + + + +functional association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +functional association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +functional association->object category closure + + +object category closure + + + +subject namespace + +string + + + +functional association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +functional association->object namespace + + +object namespace + + + +subject label closure + +string + + + +functional association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +functional association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +functional association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + functional association->type - - -type + + +type - + category - -category + +category - + functional association->category - - -category + + +category - + subject - -subject + +subject - + functional association->subject - - -subject + + +subject - + object - -object + +object - + functional association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin - + object->relation - - + + - + functional association_object - -ontology class + +ontology class diff --git a/graphviz/gene_as_a_model_of_disease_association.gv b/graphviz/gene_as_a_model_of_disease_association.gv index 334591c121..17fc494c43 100644 --- a/graphviz/gene_as_a_model_of_disease_association.gv +++ b/graphviz/gene_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4395,283"]; + graph [bb="0,0,6114,283"]; node [label="\N"]; "gene as a model of disease association" [height=0.5, label="gene as a model of disease association", - pos="2515.8,265", + pos="3435.8,265", width=5.2718]; "gene to disease association" [height=0.5, pos="137.79,178", width=3.8274]; "gene as a model of disease association" -> "gene to disease association" [label=is_a, - lp="783.79,221.5", - pos="e,234.58,190.85 2326.8,263.17 2006.3,261.11 1336,253.92 769.79,229 553.94,219.5 499.94,215.75 284.79,196 271.84,194.81 258.27,193.43 \ -244.83,191.98"]; + lp="777.79,221.5", + pos="e,234.59,190.84 3247.2,262.9 2721.7,259.61 1248,248.84 763.79,229 550.57,220.27 497.28,215.6 284.79,196 271.84,194.81 258.27,193.42 \ +244.83,191.96"]; "model to disease association mixin" [height=0.5, pos="465.79,178", width=4.7843]; "gene as a model of disease association" -> "model to disease association mixin" [label=uses, - lp="1005.3,221.5", - pos="e,575.8,191.85 2326.1,264.06 2037.2,263.15 1469.7,257.46 988.79,229 850.3,220.8 691.76,204.7 585.88,192.97"]; + lp="995.29,221.5", + pos="e,573.18,192.08 3246.4,263.34 2750,261.27 1419,253.54 978.79,229 842.82,221.42 687.22,205.18 583.38,193.26"]; "entity to disease association mixin" [height=0.5, pos="826.79,178", width=4.7482]; "gene as a model of disease association" -> "entity to disease association mixin" [label=uses, - lp="1152.3,221.5", - pos="e,902.61,194.21 2327.7,262.38 2005.6,259.07 1361.2,250 1135.8,229 1059.9,221.93 974.49,207.61 912.71,196.1"]; + lp="1151.3,221.5", + pos="e,901.4,194.24 3245.9,264.68 2771.3,265.79 1542.5,265 1134.8,229 1058.8,222.29 973.11,207.82 911.47,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "gene as a model of disease association" -> id [color=blue, label=id, - lp="1273.8,221.5", - pos="e,1082.8,190.01 2327.5,262.63 2030.4,259.81 1466.3,251.58 1266.8,229 1192.5,220.59 1173.9,215.87 1101.8,196 1098.7,195.14 1095.5,\ -194.18 1092.3,193.17", + lp="1270.8,221.5", + pos="e,1082.8,190 3247.1,262.96 2755,259.95 1457.6,250.11 1263.8,229 1190.7,221.04 1172.6,215.65 1101.8,196 1098.7,195.14 1095.5,194.17 \ +1092.3,193.16", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "gene as a model of disease association" -> iri [color=blue, label=iri, - lp="1394.8,221.5", - pos="e,1187.4,190.18 2329.3,261.64 2056.9,257.61 1563.7,247.94 1386.8,229 1306.4,220.39 1286.2,215.73 1207.8,196 1204.4,195.14 1200.8,\ -194.17 1197.3,193.16", + lp="1387.8,221.5", + pos="e,1187.7,190.23 3247.3,262.65 2774.4,258.99 1562.1,247.89 1379.8,229 1302.4,220.97 1283.2,215.26 1207.8,196 1204.4,195.14 1200.9,\ +194.18 1197.4,193.17", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "gene as a model of disease association" -> name [color=blue, label=name, - lp="1509.8,221.5", - pos="e,1313.9,190.9 2329,261.71 2078.4,257.93 1646.6,248.75 1489.8,229 1432,221.72 1367.1,205.6 1323.7,193.62", + lp="1498.8,221.5", + pos="e,1312.6,191.27 3247.2,262.94 2790.7,260.03 1650.7,250.68 1478.8,229 1424.4,222.14 1363.5,206.21 1322.4,194.16", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "gene as a model of disease association" -> description [color=blue, label=description, - lp="1636.3,221.5", - pos="e,1463.1,193.43 2328,262.27 2100.7,259.22 1731.6,250.98 1595.8,229 1553.5,222.15 1506.8,208.17 1472.8,196.73", + lp="1626.3,221.5", + pos="e,1461,193.78 3246.6,263.42 2807.8,261.65 1746.2,254.74 1585.8,229 1546,222.62 1502.5,208.77 1470.6,197.26", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "gene as a model of disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1790.8,221.5", - pos="e,1603.4,191.5 2331.7,260.59 2140,256.15 1852.6,246.76 1743.8,229 1698.5,221.61 1648.3,206.52 1613.3,194.84", + lp="1782.8,221.5", + pos="e,1602.1,191.88 3247.1,262.99 2835.4,260.36 1881.5,251.87 1735.8,229 1692.5,222.21 1644.8,207.12 1611.5,195.28", style=solid]; predicate [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=2.1665]; "gene as a model of disease association" -> predicate [color=blue, label=predicate, - lp="1945.8,221.5", - pos="e,1760.8,192.89 2327.7,262.43 2208.1,259.13 2050.1,250.53 1911.8,229 1863.4,221.47 1809.7,207.23 1770.8,195.86", + lp="1941.8,221.5", + pos="e,1759.4,193.23 3248.2,262.15 2869.1,258.06 2037,247.13 1907.8,229 1860.1,222.31 1807.3,207.91 1769.3,196.27", style=solid]; negated [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=1.2999]; "gene as a model of disease association" -> negated [color=blue, label=negated, - lp="2081.8,221.5", - pos="e,1894.6,190.23 2343.3,257.5 2255.8,252.55 2148.3,243.93 2052.8,229 2001.1,220.93 1943.3,204.98 1904.5,193.26", + lp="2083.8,221.5", + pos="e,1893.8,190.44 3246.1,264.02 2923,263.25 2279.2,257.98 2054.8,229 2001.9,222.17 1942.7,205.69 1903.6,193.51", style=solid]; qualifiers [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=2.1304]; "gene as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2212.3,221.5", - pos="e,2043.1,193.09 2365.7,253.92 2307,248.55 2239.5,240.58 2178.8,229 2135.7,220.77 2087.9,207.08 2052.7,196.11", + lp="2223.3,221.5", + pos="e,2043,193.17 3246.2,264.01 2949.2,263.13 2387.7,257.57 2189.8,229 2142.6,222.19 2090.3,207.8 2052.7,196.2", style=solid]; publications [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=1.7332]; "gene as a model of disease association" -> publications [color=blue, label=publications, - lp="2338.8,221.5", - pos="e,2191.3,193.28 2403.3,250.48 2368.3,245.12 2329.7,238.04 2294.8,229 2262.6,220.66 2227.4,207.71 2200.7,197.08", + lp="2369.8,221.5", + pos="e,2193.9,192.69 3246.2,263.91 2976.9,262.77 2497.2,256.73 2325.8,229 2283.4,222.14 2236.7,207.66 2203.3,196.04", style=solid]; "has evidence" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=2.0943]; "gene as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2465.3,221.5", - pos="e,2344.7,194.69 2467.1,247.48 2451.5,241.92 2434.3,235.48 2418.8,229 2397,219.91 2373.2,208.7 2353.8,199.2", + lp="2522.3,221.5", + pos="e,2351.4,193.7 3247.2,262.99 3010.6,260.7 2618.8,253.24 2475.8,229 2436.2,222.29 2392.8,208.54 2360.9,197.15", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "gene as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2580.3,221.5", - pos="e,2515.8,196.18 2515.8,246.8 2515.8,235.16 2515.8,219.55 2515.8,206.24", + lp="2674.3,221.5", + pos="e,2539.7,195.57 3252,260.52 3027.4,255.59 2669.8,245.33 2609.8,229 2588.1,223.09 2565.7,211.49 2548.3,200.95", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -143,8 +143,8 @@ digraph { width=3.015]; "gene as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2773.8,221.5", - pos="e,2718.5,195.23 2586.3,248.22 2606.7,242.91 2628.9,236.42 2648.8,229 2655.1,226.64 2684,212.46 2709.3,199.8", + lp="2842.8,221.5", + pos="e,2744.1,196.01 3250.8,260.82 3053,256.49 2765,247.11 2747.8,229 2742,222.91 2741,214.28 2742,205.91", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -153,9 +153,8 @@ digraph { width=3.015]; "gene as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3001.3,221.5", - pos="e,2940.1,194.43 2650.6,252.25 2746.8,243.61 2861.1,232.76 2871.8,229 2883.3,224.95 2883.9,219.55 2894.8,214 2906.1,208.22 2918.6,\ -202.83 2930.6,198.09", + lp="3051.3,221.5", + pos="e,2958.5,195.65 3247.4,262.68 3118,259.75 2965.7,251.48 2944.8,229 2936.9,220.57 2942,210.87 2950.8,202.27", style=solid]; timepoint [color=blue, height=0.5, @@ -164,9 +163,8 @@ digraph { width=1.5346]; "gene as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3164.8,221.5", - pos="e,3150.9,195.2 2647.4,252.02 2669.9,250.19 2693,248.43 2714.8,247 2758.4,244.14 3067,244.82 3107.8,229 3115.7,225.91 3130.4,213.77 \ -3143.2,202.23", + lp="3201.8,221.5", + pos="e,3162.1,196.29 3291.3,253.33 3232.4,247.48 3175.8,239.31 3166.8,229 3161.4,222.85 3160.1,214.46 3160.6,206.3", style=solid]; "original subject" [color=blue, height=0.5, @@ -175,9 +173,8 @@ digraph { width=1.0652]; "gene as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3279.8,221.5", - pos="e,3257.7,192.7 2646.6,251.92 2669.3,250.08 2692.7,248.35 2714.8,247 2768.7,243.7 3149.3,245.35 3200.8,229 3212.4,225.31 3213.5,220.57 \ -3223.8,214 3231.9,208.79 3240.8,203.21 3249,198.07", + lp="3299.8,221.5", + pos="e,3258.7,193.19 3302.1,252.16 3275.3,247 3252.6,239.6 3243.8,229 3236.2,219.86 3242,209.22 3251,200.11", style=solid]; "original predicate" [color=blue, height=0.5, @@ -186,9 +183,8 @@ digraph { width=1.5887]; "gene as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3421.3,221.5", - pos="e,3377.2,195.5 2645.5,251.86 2668.6,250 2692.4,248.28 2714.8,247 2783.7,243.06 3271.4,253.98 3335.8,229 3343.5,225.99 3357.6,213.99 \ -3369.9,202.5", + lp="3425.3,221.5", + pos="e,3373,195.19 3381.9,247.66 3373.9,242.9 3366.7,236.8 3361.8,229 3356.4,220.42 3359.8,211.04 3366.2,202.75", style=solid]; "original object" [color=blue, height=0.5, @@ -197,107 +193,225 @@ digraph { width=1.0652]; "gene as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3550.3,221.5", - pos="e,3505,196.44 2645,251.79 2668.2,249.93 2692.2,248.23 2714.8,247 2757.6,244.68 3450.2,252.83 3485.8,229 3493.7,223.71 3498.8,214.9 \ -3502,206.13", + lp="3549.3,221.5", + pos="e,3504.1,196.09 3468.1,247.25 3475.7,242.19 3483.1,236.06 3488.8,229 3494.2,222.27 3498.2,213.85 3501,205.85", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3640.8,178", + width=2.1304]; + "gene as a model of disease association" -> "subject category" [color=blue, + label="subject category", + lp="3680.3,221.5", + pos="e,3632.8,195.96 3555.2,250.94 3572.7,245.79 3589.8,238.7 3604.8,229 3614.1,222.97 3621.7,213.65 3627.6,204.68", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3811.8,178", + width=2.1304]; + "gene as a model of disease association" -> "object category" [color=blue, + label="object category", + lp="3826.3,221.5", + pos="e,3794.6,195.64 3568.8,252.09 3644.3,244.76 3727.1,235.54 3743.8,229 3759.4,222.87 3774.7,212.22 3786.8,202.31", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3944.8,178", + width=1.0652]; + "gene as a model of disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3964.3,221.5", + pos="e,3931.1,195.14 3570.1,252.27 3591.7,250.46 3613.9,248.64 3634.8,247 3690.5,242.62 3834,250.12 3885.8,229 3900.1,223.18 3913.4,212.53 \ +3923.8,202.55", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4040.8,178", + width=1.0652]; + "gene as a model of disease association" -> "object closure" [color=blue, + label="object closure", + lp="4084.8,221.5", + pos="e,4039.4,196.26 3567.4,252.03 3589.9,250.19 3613,248.44 3634.8,247 3677.9,244.16 3988.1,254.63 4022.8,229 4030.2,223.57 4034.5,214.84 \ +4037.1,206.18", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4173.8,178", + width=2.1304]; + "gene as a model of disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4243.3,221.5", + pos="e,4166.8,196.13 3566.3,251.92 3589.1,250.07 3612.6,248.34 3634.8,247 3690.7,243.61 4089.6,255.76 4138.8,229 4148.6,223.69 4156.2,\ +214.32 4161.8,205.12", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4365.8,178", + width=2.1304]; + "gene as a model of disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4433.3,221.5", + pos="e,4360.1,196.11 3565.2,251.82 3588.4,249.96 3612.3,248.25 3634.8,247 3673.6,244.84 4301,248.35 4334.8,229 4344,223.72 4350.8,214.49 \ +4355.7,205.38", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4555.8,178", + width=1.0652]; + "gene as a model of disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4605.8,221.5", + pos="e,4548.8,196.19 3564.7,251.76 3588,249.9 3612.1,248.2 3634.8,247 3684,244.4 4477.4,252.18 4520.8,229 4530.6,223.76 4538.3,214.41 \ +4543.9,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4714.8,178", + width=1.0652]; + "gene as a model of disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4758.8,221.5", + pos="e,4707.4,195.74 3564.4,251.72 3587.8,249.86 3612,248.17 3634.8,247 3663.7,245.52 4652,242.26 4677.8,229 4688.1,223.68 4696.3,214 \ +4702.3,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4865.8,178", + width=1.0652]; + "gene as a model of disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4918.8,221.5", + pos="e,4857.8,195.77 3564.2,251.7 3587.6,249.83 3611.9,248.15 3634.8,247 3667.9,245.34 4797.1,243.75 4826.8,229 4837.5,223.67 4846.2,\ +213.85 4852.6,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5036.8,178", + width=1.0652]; + "gene as a model of disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="5084.3,221.5", + pos="e,5028.5,195.79 3563.9,251.69 3587.4,249.81 3611.8,248.13 3634.8,247 3672.6,245.14 4962.8,245.62 4996.8,229 5007.6,223.69 5016.5,\ +213.88 5023.1,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5180.8,178", + width=2.347]; + "gene as a model of disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5240.3,221.5", + pos="e,5177.8,196.01 3563.6,251.68 3587.3,249.8 3611.8,248.12 3634.8,247 3677,244.95 5122.3,252.04 5157.8,229 5165.9,223.71 5171.2,214.73 \ +5174.7,205.83", style=solid]; type [height=0.5, - pos="3595.8,178", + pos="5314.8,178", width=0.86659]; "gene as a model of disease association" -> type [color=blue, label=type, - lp="3627.8,221.5", - pos="e,3605.7,195.51 2644.7,251.76 2668,249.89 2692.1,248.2 2714.8,247 2739.5,245.7 3588.5,246.68 3605.8,229 3612,222.66 3611.8,213.62 \ -3609.3,204.96", + lp="5336.8,221.5", + pos="e,5319.9,196.18 3563.6,251.66 3587.3,249.78 3611.8,248.11 3634.8,247 3658.1,245.88 5297.2,245.41 5313.8,229 5319.8,223.09 5321.4,\ +214.51 5321,206.13", style=solid]; category [height=0.5, - pos="3696.8,178", + pos="5415.8,178", width=1.4263]; "gene as a model of disease association" -> category [color=blue, label=category, - lp="3701.3,221.5", - pos="e,3685.7,195.85 2644.4,251.76 2667.8,249.89 2692,248.19 2714.8,247 2766.6,244.29 3600.2,249.54 3647.8,229 3660.2,223.66 3671,213.56 \ -3679.3,203.82", + lp="5414.3,221.5", + pos="e,5402.2,195.46 3563.6,251.66 3587.3,249.78 3611.8,248.1 3634.8,247 3682.6,244.71 5312,245.71 5356.8,229 5371.4,223.57 5384.8,212.81 \ +5395.2,202.66", style=solid]; object [height=0.5, - pos="4279.8,91", + pos="5998.8,91", width=1.0832]; "gene as a model of disease association" -> object [color=blue, label=object, - lp="3814.8,178", - pos="e,4241.2,93.765 2644.4,251.73 2667.8,249.86 2692,248.17 2714.8,247 2771.5,244.08 3685.7,253.87 3736.8,229 3772.3,211.7 3758.4,179.41 \ -3792.8,160 3867.2,118.02 4122.8,100.12 4230.9,94.306", + lp="5533.8,178", + pos="e,5960.3,93.981 3563.4,251.67 3587.1,249.78 3611.7,248.1 3634.8,247 3685.1,244.6 5403.8,249.76 5449.8,229 5487.4,212.03 5475.4,179.36 \ +5511.8,160 5587.2,119.9 5842.2,100.94 5950,94.576", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3930.8,178", + pos="5649.8,178", width=2.3651]; "gene as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3918.8,221.5", - pos="e,3898.4,194.79 2644.2,251.73 2667.6,249.86 2691.9,248.16 2714.8,247 2835,240.87 3679.6,251.51 3797.8,229 3829.4,222.99 3863.3,210.13 \ -3888.9,198.97", + lp="5637.8,221.5", + pos="e,5617.6,194.73 3563.4,251.66 3587.1,249.78 3611.7,248.1 3634.8,247 3739.2,242.05 5414,248.19 5516.8,229 5548.5,223.08 5582.5,210.16 \ +5608.2,198.93", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4109.8,178", + pos="5828.8,178", width=2.1123]; "gene as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4099.8,221.5", - pos="e,4081,194.81 2643.9,251.71 2667.4,249.83 2691.8,248.14 2714.8,247 2856.4,239.96 3852,257.99 3990.8,229 4019.1,223.08 4049.2,210.4 \ -4072,199.29", + lp="5818.8,221.5", + pos="e,5800,194.86 3563.4,251.65 3587.1,249.76 3611.7,248.09 3634.8,247 3749.9,241.59 5596.9,252.27 5709.8,229 5738.1,223.16 5768.2,210.48 \ +5791,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4239.8,178", + pos="5958.8,178", width=1.011]; "gene as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4247.3,221.5", - pos="e,4223.1,194.29 2643.6,251.7 2667.3,249.81 2691.8,248.13 2714.8,247 2795.3,243.07 4087.8,252.82 4164.8,229 4183.2,223.29 4201.3,\ -211.47 4215.1,200.75", + lp="5966.3,221.5", + pos="e,5942.4,194.07 3563.3,251.63 3587.1,249.75 3611.7,248.08 3634.8,247 3697.2,244.09 5824.1,247.34 5883.8,229 5902.4,223.29 5920.6,\ +211.35 5934.4,200.57", style=solid]; subject [height=0.5, - pos="4350.8,178", + pos="6069.8,178", width=1.2277]; "gene as a model of disease association" -> subject [color=blue, label=subject, - lp="4349.8,221.5", - pos="e,4340,195.88 2643.6,251.67 2667.3,249.79 2691.8,248.11 2714.8,247 2758.9,244.87 4262.3,246.53 4302.8,229 4315,223.7 4325.7,213.6 \ -4333.8,203.86", + lp="6068.8,221.5", + pos="e,6059,195.89 3563.1,251.65 3586.9,249.75 3611.6,248.08 3634.8,247 3701,243.93 5960.9,255.23 6021.8,229 6034,223.72 6044.7,213.63 \ +6052.8,203.88", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2761.8,265", + pos="3681.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2892.8,265", + pos="3812.8,265", width=2.0762]; relation [height=0.5, - pos="4314.8,18", + pos="6033.8,18", width=1.2999]; - object -> relation [pos="e,4306.3,36.198 4288.1,73.174 4292.2,64.896 4297.2,54.723 4301.8,45.438", + object -> relation [pos="e,6025.3,36.198 6007.1,73.174 6011.2,64.896 6016.2,54.723 6020.8,45.438", style=dotted]; "gene to disease association_object" [color=blue, height=0.5, label=disease, - pos="3030.8,265", + pos="3950.8,265", width=1.2638]; subject -> object [label=relation, - lp="4308.8,134.5", - pos="e,4276,109.01 4314.4,167.42 4301.6,162.12 4288.4,154.06 4280.8,142 4276.5,135.26 4275.2,126.93 4275.2,119.01"]; - subject -> relation [pos="e,4319,36.005 4347.1,160.05 4342.7,139.44 4334.9,103.63 4327.8,73 4325.8,64.183 4323.5,54.574 4321.4,45.938", + lp="6027.8,134.5", + pos="e,5995,109.01 6033.4,167.42 6020.6,162.12 6007.4,154.06 5999.8,142 5995.5,135.26 5994.2,126.93 5994.2,119.01"]; + subject -> relation [pos="e,6038,36.005 6066.1,160.05 6061.7,139.44 6053.9,103.63 6046.8,73 6044.8,64.183 6042.5,54.574 6040.4,45.938", style=dotted]; "gene as a model of disease association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3204.8,265", + pos="4124.8,265", width=3.0692]; } diff --git a/graphviz/gene_as_a_model_of_disease_association.svg b/graphviz/gene_as_a_model_of_disease_association.svg index c3ea14ac89..03b9ec3438 100644 --- a/graphviz/gene_as_a_model_of_disease_association.svg +++ b/graphviz/gene_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene as a model of disease association - -gene as a model of disease association + +gene as a model of disease association @@ -24,9 +24,9 @@ gene as a model of disease association->gene to disease association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene as a model of disease association->model to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ gene as a model of disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ gene as a model of disease association->id - - -id + + +id @@ -76,9 +76,9 @@ gene as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ gene as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ gene as a model of disease association->description - - -description + + +description @@ -115,9 +115,9 @@ gene as a model of disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ gene as a model of disease association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ gene as a model of disease association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ gene as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ gene as a model of disease association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ gene as a model of disease association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ gene as a model of disease association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ gene as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ gene as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ gene as a model of disease association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ gene as a model of disease association->original subject - - -original subject + + +original subject @@ -258,9 +258,9 @@ gene as a model of disease association->original predicate - - -original predicate + + +original predicate @@ -271,149 +271,292 @@ gene as a model of disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene as a model of disease association->subject category + + +subject category + + + +object category + +ontology class + + + +gene as a model of disease association->object category + + +object category + + + +subject closure + +string + + + +gene as a model of disease association->subject closure + + +subject closure + + + +object closure + +string + + + +gene as a model of disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene as a model of disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene as a model of disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene as a model of disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene as a model of disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene as a model of disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene as a model of disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene as a model of disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene as a model of disease association->type - - -type + + +type - + category - -category + +category - + gene as a model of disease association->category - - -category + + +category - + object - -object + +object - + gene as a model of disease association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + gene as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + gene as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + gene as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + subject - -subject + +subject - + gene as a model of disease association->subject - - -subject + + +subject - + association_type - -string + +string - + association_category - -category type + +category type - + relation - -relation + +relation - + object->relation - - + + - + gene to disease association_object - -disease + +disease - + subject->object - - -relation + + +relation - + subject->relation - - + + - + gene as a model of disease association_subject - -gene or gene product + +gene or gene product diff --git a/graphviz/gene_has_variant_that_contributes_to_disease_association.gv b/graphviz/gene_has_variant_that_contributes_to_disease_association.gv index ab7966cbba..1d54b757fd 100644 --- a/graphviz/gene_has_variant_that_contributes_to_disease_association.gv +++ b/graphviz/gene_has_variant_that_contributes_to_disease_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3847.4,283"]; + graph [bb="0,0,5567.4,283"]; node [label="\N"]; "gene has variant that contributes to disease association" [height=0.5, label="gene has variant that contributes to disease association", - pos="2137.8,265", + pos="2886.8,265", width=7.5104]; "gene to disease association" [height=0.5, pos="137.79,178", width=3.8274]; "gene has variant that contributes to disease association" -> "gene to disease association" [label=is_a, lp="430.79,221.5", - pos="e,203.9,193.87 1867.9,263.68 1456.1,262.31 689.73,256.06 416.79,229 347.49,222.13 269.56,207.58 213.71,195.94"]; + pos="e,203.32,193.87 2618.5,262.67 2023.8,259.37 630.7,249.55 416.79,229 347.24,222.32 269.02,207.67 213.14,195.95"]; id [color=blue, height=0.5, label=string, @@ -19,8 +19,8 @@ digraph { "gene has variant that contributes to disease association" -> id [color=blue, label=id, lp="546.79,221.5", - pos="e,360.77,189.98 1867.7,264.01 1481,263.01 788.64,257.15 539.79,229 467.64,220.84 449.73,215.5 379.79,196 376.68,195.13 373.48,194.17 \ -370.28,193.15", + pos="e,360.77,189.98 2618.2,262.85 2045.7,259.97 741.16,251.07 539.79,229 467.61,221.09 449.73,215.5 379.79,196 376.68,195.13 373.48,\ +194.17 370.28,193.15", style=solid]; iri [color=blue, height=0.5, @@ -30,7 +30,7 @@ digraph { "gene has variant that contributes to disease association" -> iri [color=blue, label=iri, lp="659.79,221.5", - pos="e,465.7,190.2 1868.5,263.23 1505.8,261.23 879.43,254.12 651.79,229 577.02,220.75 558.61,214.85 485.79,196 482.41,195.13 478.93,194.16 \ + pos="e,465.7,190.2 2618.8,262.52 2067.6,259.08 842.2,249.25 651.79,229 576.99,221.05 558.61,214.85 485.79,196 482.41,195.13 478.93,194.16 \ 475.45,193.15", style=solid]; name [color=blue, @@ -41,7 +41,7 @@ digraph { "gene has variant that contributes to disease association" -> name [color=blue, label=name, lp="766.79,221.5", - pos="e,589.76,191.47 1867.4,264.42 1525.2,263.69 955.41,257.93 746.79,229 695.68,221.91 638.66,206.37 599.55,194.48", + pos="e,589.38,191.45 2617.7,263.12 2084,260.86 927.1,253.2 746.79,229 695.49,222.12 638.27,206.46 599.16,194.49", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene has variant that contributes to disease association" -> description [color=blue, label=description, - lp="888.29,221.5", - pos="e,736.1,194.07 1873.7,261.1 1525.5,256.61 945.42,246.62 847.79,229 812.37,222.61 773.93,209.16 745.38,197.82", + lp="887.29,221.5", + pos="e,735.84,194.17 2616.5,264.09 2101.7,263.56 1016.1,258.86 846.79,229 811.72,222.81 773.72,209.45 745.42,198.09", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene has variant that contributes to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1034.8,221.5", - pos="e,876.84,192.74 1876.6,260.32 1564.1,255.24 1072.4,244.88 987.79,229 952.39,222.35 913.98,208.24 886.2,196.7", + lp="1032.8,221.5", + pos="e,876.37,192.85 2616.6,263.9 2129.8,263 1141.4,257.61 985.79,229 950.82,222.57 912.95,208.44 885.59,196.83", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene has variant that contributes to disease association" -> negated [color=blue, label=negated, - lp="1191.8,221.5", - pos="e,998.19,190.23 1877.1,260.2 1636,255.68 1295.5,246.43 1162.8,229 1108.6,221.88 1047.8,205.32 1007.9,193.21", + lp="1187.8,221.5", + pos="e,997.8,190.49 2620.8,261.7 2172,257.37 1299.3,246.78 1158.8,229 1105.8,222.3 1046.7,205.8 1007.5,193.58", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene has variant that contributes to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1325.3,221.5", - pos="e,1146.9,193.12 1880.1,259.54 1673.6,254.82 1401,245.65 1291.8,229 1245.3,221.91 1193.7,207.62 1156.5,196.13", + lp="1327.3,221.5", + pos="e,1146.6,193.12 2621.1,261.59 2201.7,257.28 1420.9,246.96 1293.8,229 1246.4,222.31 1193.9,207.84 1156.3,196.18", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene has variant that contributes to disease association" -> publications [color=blue, label=publications, - lp="1463.8,221.5", - pos="e,1296.9,192.99 1885.3,258.55 1715,253.57 1506.3,244.53 1419.8,229 1380.7,221.98 1337.8,207.99 1306.6,196.59", + lp="1473.8,221.5", + pos="e,1297.8,192.77 2621.6,261.43 2233.4,257.09 1543.6,246.98 1429.8,229 1387.4,222.3 1340.7,207.8 1307.3,196.13", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "gene has variant that contributes to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="1611.3,221.5", - pos="e,1453,193.95 1903.5,255.97 1774.6,250.31 1628.2,241.49 1564.8,229 1529.5,222.05 1491.1,208.76 1462.4,197.63", + lp="1634.3,221.5", + pos="e,1456.6,193.56 2616.3,264.93 2295,264.59 1778.5,259.1 1587.8,229 1545.9,222.39 1499.8,208.39 1466.2,196.89", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "gene has variant that contributes to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1752.3,221.5", - pos="e,1636.9,195.85 1895.7,256.95 1810.8,251.98 1726.8,243.48 1687.8,229 1672.1,223.15 1656.8,212.52 1644.7,202.57", + lp="1792.3,221.5", + pos="e,1647.5,195.66 2621.2,261.59 2305.9,257.85 1812,248.89 1727.8,229 1702.9,223.11 1676.7,211.2 1656.4,200.47", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "gene has variant that contributes to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1918.8,221.5", - pos="e,1833.7,195.76 1942.9,252.48 1884.4,247.02 1833.1,239.37 1823.8,229 1816.9,221.31 1820.3,211.9 1826.9,203.32", + lp="1965.8,221.5", + pos="e,1855.5,196.24 2619.3,262.36 2328.3,259.44 1900.3,251.36 1870.8,229 1863.6,223.55 1859.6,214.81 1857.3,206.16", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "gene has variant that contributes to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2127.3,221.5", - pos="e,2043.1,194.29 2043.1,248.09 2034.4,243.23 2026.7,236.99 2020.8,229 2012,217.21 2020.4,207.04 2034,199.01", + lp="2175.3,221.5", + pos="e,2074.1,196.04 2622,261.37 2390.4,257.72 2088.1,249.11 2068.8,229 2062.3,222.24 2064,213.18 2068.6,204.64", style=solid]; timepoint [color=blue, height=0.5, @@ -140,8 +140,8 @@ digraph { width=1.5346]; "gene has variant that contributes to disease association" -> timepoint [color=blue, label=timepoint, - lp="2283.8,221.5", - pos="e,2262.4,195.86 2199.6,247.39 2211.6,242.58 2223.6,236.53 2233.8,229 2242.7,222.4 2250.6,213.12 2256.8,204.35", + lp="2333.8,221.5", + pos="e,2276.4,196.41 2626.6,260.09 2482.7,255.88 2327.2,247.14 2298.8,229 2290.4,223.63 2284.4,214.67 2280.2,205.81", style=solid]; "original subject" [color=blue, height=0.5, @@ -150,8 +150,8 @@ digraph { width=1.0652]; "gene has variant that contributes to disease association" -> "original subject" [color=blue, label="original subject", - lp="2402.8,221.5", - pos="e,2368.8,195.02 2263.4,249.05 2283.8,244.15 2304.3,237.64 2322.8,229 2337,222.38 2350.6,211.71 2361.4,201.92", + lp="2433.8,221.5", + pos="e,2375.7,195.93 2622,261.24 2507.7,257.24 2395.8,248.32 2377.8,229 2372,222.82 2371.5,214.18 2373,205.81", style=solid]; "original predicate" [color=blue, height=0.5, @@ -160,8 +160,8 @@ digraph { width=1.5887]; "gene has variant that contributes to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="2542.3,221.5", - pos="e,2490.3,195.85 2352.2,254.02 2399.3,248.83 2441.3,240.96 2461.8,229 2471.5,223.35 2479.3,213.92 2485.1,204.77", + lp="2563.3,221.5", + pos="e,2493.3,196.02 2657.4,255.43 2581.1,250.24 2512.2,242 2499.8,229 2494.1,222.98 2492.3,214.48 2492.4,206.19", style=solid]; "original object" [color=blue, height=0.5, @@ -170,131 +170,246 @@ digraph { width=1.0652]; "gene has variant that contributes to disease association" -> "original object" [color=blue, label="original object", - lp="2668.3,221.5", - pos="e,2616.3,196.06 2332.2,252.48 2460,244.44 2604.7,234.24 2609.8,229 2615.6,223.03 2617.3,214.54 2617.2,206.25", + lp="2697.3,221.5", + pos="e,2619,196.18 2726.4,250.49 2691.6,245.34 2660.8,238.36 2645.8,229 2636.6,223.24 2629.3,213.96 2623.8,204.96", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2744.8,178", + width=2.1304]; + "gene has variant that contributes to disease association" -> "subject category" [color=blue, + label="subject category", + lp="2821.3,221.5", + pos="e,2746.5,196.01 2791.4,248.09 2780.5,243.28 2770.3,237.06 2761.8,229 2755.4,222.91 2751.4,214.28 2748.9,205.91", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2915.8,178", + width=2.1304]; + "gene has variant that contributes to disease association" -> "object category" [color=blue, + label="object category", + lp="2943.3,221.5", + pos="e,2898.7,195.76 2884.5,246.84 2883.8,236.95 2884,224.45 2887.8,214 2889.1,210.5 2890.8,207.09 2892.9,203.85", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3048.8,178", + width=1.0652]; + "gene has variant that contributes to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3072.3,221.5", + pos="e,3036,195.49 2957.4,247.62 2971.7,242.77 2986.2,236.65 2998.8,229 3010.1,222.15 3020.8,212.2 3029.3,202.98", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3147.8,178", + width=1.0652]; + "gene has variant that contributes to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3191.8,221.5", + pos="e,3146.4,196.41 3063.5,251.31 3093.4,246.21 3118.7,239.04 3130.8,229 3137.6,223.34 3141.7,214.82 3144.2,206.41", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3280.8,178", + width=2.1304]; + "gene has variant that contributes to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3349.3,221.5", + pos="e,3273.4,196.38 3077.6,252.24 3155.1,246.19 3230.1,238.15 3245.8,229 3255.3,223.47 3262.8,214.24 3268.4,205.2", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3473.8,178", + width=2.1304]; + "gene has variant that contributes to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="3540.3,221.5", + pos="e,3467.4,196 3079.2,252.34 3238.4,242.61 3438.8,230.16 3440.8,229 3450.2,223.52 3457.5,214.13 3462.8,204.95", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3663.8,178", + width=1.0652]; + "gene has variant that contributes to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3712.8,221.5", + pos="e,3656.4,196.13 3074.6,252.03 3105.4,250.23 3137,248.49 3166.8,247 3218,244.45 3582.6,253.26 3627.8,229 3637.8,223.63 3645.7,214.12 \ +3651.5,204.83", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3822.8,178", + width=1.0652]; + "gene has variant that contributes to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="3865.8,221.5", + pos="e,3815.1,195.7 3072.4,251.91 3103.9,250.09 3136.3,248.37 3166.8,247 3201.1,245.46 3754.2,244.71 3784.8,229 3795.2,223.63 3803.6,\ +213.94 3809.8,204.51", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3973.8,178", + width=1.0652]; + "gene has variant that contributes to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4025.8,221.5", + pos="e,3965.5,195.75 3071.2,251.82 3103.1,250 3135.9,248.3 3166.8,247 3209.4,245.21 3895.6,247.91 3933.8,229 3944.6,223.64 3953.5,213.81 \ +3960.1,204.28", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4144.8,178", + width=1.0652]; + "gene has variant that contributes to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4191.3,221.5", + pos="e,4136.2,195.78 3070.5,251.76 3102.6,249.93 3135.6,248.24 3166.8,247 3218.8,244.92 4056.9,251.72 4103.8,229 4114.8,223.67 4123.8,\ +213.85 4130.6,204.32", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4285.8,178", + width=2.347]; + "gene has variant that contributes to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4347.3,221.5", + pos="e,4283.4,196.44 3069.7,251.72 3102.1,249.89 3135.4,248.21 3166.8,247 3197.3,245.83 4239.5,246.09 4264.8,229 4272.6,223.71 4277.5,\ +214.89 4280.6,206.13", style=solid]; type [height=0.5, - pos="2699.8,178", + pos="4419.8,178", width=0.86659]; "gene has variant that contributes to disease association" -> type [color=blue, label=type, - lp="2744.8,221.5", - pos="e,2715.4,194 2329.8,252.29 2359.3,250.51 2389.3,248.7 2417.8,247 2451.8,244.97 2700.4,253.78 2723.8,229 2731,221.38 2727.7,211.22 \ -2721.6,202.04", + lp="4443.8,221.5", + pos="e,4425.7,196.12 3069.4,251.69 3101.8,249.85 3135.3,248.18 3166.8,247 3184.2,246.35 4408.6,241.4 4420.8,229 4426.7,223.02 4428,214.43 \ +4427.3,206.04", style=solid]; category [height=0.5, - pos="2800.8,178", + pos="4520.8,178", width=1.4263]; "gene has variant that contributes to disease association" -> category [color=blue, label=category, - lp="2813.3,221.5", - pos="e,2793.4,196.08 2328.3,252.21 2358.2,250.42 2388.9,248.63 2417.8,247 2456.3,244.83 2730.9,247.49 2764.8,229 2774.6,223.62 2782.5,\ -214.24 2788.3,205.05", + lp="4520.3,221.5", + pos="e,4507.8,195.43 3069.3,251.68 3101.8,249.84 3135.3,248.17 3166.8,247 3238.8,244.32 4396.5,254.86 4463.8,229 4477.9,223.58 4490.8,\ +212.97 4500.8,202.92", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="2954.8,178", + pos="4674.8,178", width=2.3651]; "gene has variant that contributes to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="2959.8,221.5", - pos="e,2928,195.32 2326.4,252.06 2356.9,250.27 2388.2,248.51 2417.8,247 2513.5,242.1 2755.7,251.9 2848.8,229 2873.3,222.96 2899.1,210.99 \ -2919,200.28", + lp="4671.8,221.5", + pos="e,4645.5,195.07 3069,251.68 3101.5,249.83 3135.2,248.16 3166.8,247 3243.9,244.16 4480.2,244.74 4555.8,229 4583.9,223.14 4613.8,210.59 \ +4636.5,199.53", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="3133.8,178", + pos="4853.8,178", width=2.1123]; "gene has variant that contributes to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="3133.8,221.5", - pos="e,3108.5,195.18 2323.8,251.89 2355.1,250.08 2387.4,248.37 2417.8,247 2486,243.93 2965.5,245.39 3031.8,229 3055.8,223.07 3080.7,210.99 \ -3099.9,200.18", + lp="4848.8,221.5", + pos="e,4826.9,195.08 3068.6,251.66 3101.3,249.81 3135,248.14 3166.8,247 3254.3,243.84 4658.3,248.04 4743.8,229 4769.8,223.2 4797.1,210.83 \ +4818,199.84", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="3263.8,178", + pos="4983.8,178", width=1.011]; "gene has variant that contributes to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="3278.3,221.5", - pos="e,3249,194.93 2322.2,251.81 2354.1,249.99 2386.9,248.29 2417.8,247 2461.2,245.18 3157.9,243.45 3198.8,229 3214.7,223.38 3229.8,212.23 \ -3241.5,201.88", + lp="4995.3,221.5", + pos="e,4968.1,194.53 3068.2,251.65 3101,249.8 3134.9,248.13 3166.8,247 3215.3,245.28 4867.6,244.05 4913.8,229 4931,223.38 4947.7,211.84 \ +4960.4,201.27", style=solid]; "subject form or variant qualifier" [color=blue, height=0.5, label=string, - pos="3356.8,178", + pos="5076.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "subject form or variant qualifier" [color=blue, label="subject form or variant qualifier", - lp="3461.3,221.5", - pos="e,3353.8,195.98 2321.5,251.77 2353.6,249.94 2386.6,248.25 2417.8,247 2443.2,245.98 3312.5,242.94 3333.8,229 3341.9,223.68 3347.2,\ -214.69 3350.7,205.79", + lp="5179.3,221.5", + pos="e,5072.8,196.08 3068.2,251.63 3101,249.78 3134.9,248.12 3166.8,247 3192.9,246.08 5028.5,242.69 5050.8,229 5059.4,223.74 5065.2,214.64 \ +5069.2,205.63", style=solid]; subject [height=0.5, - pos="3595.8,178", + pos="5315.8,178", width=1.2277]; "gene has variant that contributes to disease association" -> subject [color=blue, label=subject, - lp="3616.8,221.5", - pos="e,3595.2,196.3 2320.4,251.72 2352.8,249.88 2386.3,248.2 2417.8,247 2450,245.77 3553.9,248.23 3579.8,229 3587,223.61 3591.1,214.9 \ -3593.3,206.24", + lp="5335.8,221.5", + pos="e,5314.5,196.38 3067.8,251.62 3100.8,249.77 3134.8,248.11 3166.8,247 3196.4,245.98 5273.6,246.12 5297.8,229 5305.3,223.71 5309.6,\ +215.01 5312.2,206.34", style=solid]; object [height=0.5, - pos="3638.8,91", + pos="5358.8,91", width=1.0832]; "gene has variant that contributes to disease association" -> object [color=blue, label=object, - lp="3694.8,178", - pos="e,3652.2,108.09 2320.4,251.7 2352.8,249.86 2386.3,248.19 2417.8,247 2451.9,245.72 3620.8,251.19 3646.8,229 3681.6,199.22 3674.9,\ -170.9 3661.8,127 3660.8,123.55 3659.3,120.13 3657.5,116.85", + lp="5414.8,178", + pos="e,5372.2,108.09 3067.8,251.61 3100.8,249.76 3134.8,248.1 3166.8,247 3197.3,245.95 5342.4,248.64 5365.8,229 5400.9,199.49 5394.9,\ +170.96 5381.8,127 5380.8,123.55 5379.3,120.13 5377.5,116.85", style=solid]; predicate [height=0.5, - pos="3792.8,178", + pos="5512.8,178", width=1.5165]; "gene has variant that contributes to disease association" -> predicate [color=blue, label=predicate, - lp="3765.8,221.5", - pos="e,3769,194.32 2320.4,251.69 2352.8,249.85 2386.3,248.18 2417.8,247 2488.4,244.36 3621,245.32 3689.8,229 3714.7,223.1 3740.5,210.5 \ -3760.1,199.43", + lp="5485.8,221.5", + pos="e,5489,194.36 3067.8,251.61 3100.8,249.76 3134.8,248.1 3166.8,247 3229.1,244.86 5349.1,243.2 5409.8,229 5434.7,223.17 5460.6,210.58 \ +5480.2,199.49", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2464.8,265", + pos="3213.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2595.8,265", + pos="3344.8,265", width=2.0762]; subject -> object [label=relation, - lp="3633.8,134.5", - pos="e,3620.9,107.23 3596.9,159.55 3598.1,149.57 3600.6,137.07 3605.8,127 3608,122.68 3610.9,118.52 3614.1,114.66"]; + lp="5353.8,134.5", + pos="e,5340.9,107.23 5316.9,159.55 5318.1,149.57 5320.6,137.07 5325.8,127 5328,122.68 5330.9,118.52 5334.1,114.66"]; relation [height=0.5, - pos="3583.8,18", + pos="5303.8,18", width=1.2999]; - subject -> relation [pos="e,3585.1,36.188 3594.5,159.79 3592.4,132.48 3588.3,78.994 3585.9,46.38", + subject -> relation [pos="e,5305.1,36.188 5314.5,159.79 5312.4,132.48 5308.3,78.994 5305.9,46.38", style=dotted]; "gene has variant that contributes to disease association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2798.8,265", + pos="3547.8,265", width=3.0692]; - object -> relation [pos="e,3596.6,35.54 3626.3,73.889 3619.4,64.939 3610.6,53.617 3602.8,43.584", + object -> relation [pos="e,5316.6,35.54 5346.3,73.889 5339.4,64.939 5330.6,53.617 5322.8,43.584", style=dotted]; "gene has variant that contributes to disease association_object" [color=blue, height=0.5, label=disease, - pos="2972.8,265", + pos="3721.8,265", width=1.2638]; "gene has variant that contributes to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3113.8,265", + pos="3862.8,265", width=2.1665]; } diff --git a/graphviz/gene_has_variant_that_contributes_to_disease_association.svg b/graphviz/gene_has_variant_that_contributes_to_disease_association.svg index f6fc361b05..0294bffe2d 100644 --- a/graphviz/gene_has_variant_that_contributes_to_disease_association.svg +++ b/graphviz/gene_has_variant_that_contributes_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene has variant that contributes to disease association - -gene has variant that contributes to disease association + +gene has variant that contributes to disease association @@ -24,8 +24,8 @@ gene has variant that contributes to disease association->gene to disease association - - + + is_a @@ -37,7 +37,7 @@ gene has variant that contributes to disease association->id - + id @@ -50,7 +50,7 @@ gene has variant that contributes to disease association->iri - + iri @@ -63,8 +63,8 @@ gene has variant that contributes to disease association->name - - + + name @@ -76,9 +76,9 @@ gene has variant that contributes to disease association->description - - -description + + +description @@ -89,9 +89,9 @@ gene has variant that contributes to disease association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene has variant that contributes to disease association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene has variant that contributes to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene has variant that contributes to disease association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ gene has variant that contributes to disease association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ gene has variant that contributes to disease association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ gene has variant that contributes to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ gene has variant that contributes to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ gene has variant that contributes to disease association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ gene has variant that contributes to disease association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ gene has variant that contributes to disease association->original predicate - - -original predicate + + +original predicate @@ -232,181 +232,324 @@ gene has variant that contributes to disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene has variant that contributes to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +gene has variant that contributes to disease association->object category + + +object category + + + +subject closure + +string + + + +gene has variant that contributes to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +gene has variant that contributes to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene has variant that contributes to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene has variant that contributes to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene has variant that contributes to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene has variant that contributes to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene has variant that contributes to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene has variant that contributes to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene has variant that contributes to disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene has variant that contributes to disease association->type - - -type + + +type - + category - -category + +category - + gene has variant that contributes to disease association->category - - -category + + +category - + frequency qualifier - -frequency value + +frequency value - + gene has variant that contributes to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + gene has variant that contributes to disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + gene has variant that contributes to disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + subject form or variant qualifier - -string + +string - + gene has variant that contributes to disease association->subject form or variant qualifier - - -subject form or variant qualifier + + +subject form or variant qualifier - + subject - -subject + +subject - + gene has variant that contributes to disease association->subject - - -subject + + +subject - + object - -object + +object - + gene has variant that contributes to disease association->object - - -object + + +object - + predicate - -predicate + +predicate - + gene has variant that contributes to disease association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene has variant that contributes to disease association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene has variant that contributes to disease association_object - -disease + +disease - + gene has variant that contributes to disease association_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_disease_association.gv b/graphviz/gene_to_disease_association.gv index 170618f39e..072b7297b9 100644 --- a/graphviz/gene_to_disease_association.gv +++ b/graphviz/gene_to_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4231.4,283"]; + graph [bb="0,0,5950.4,283"]; node [label="\N"]; "gene to disease association" [height=0.5, label="gene to disease association", - pos="2339.4,265", + pos="3259.4,265", width=3.8274]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to disease association" -> association [label=is_a, - lp="618.39,221.5", - pos="e,106.48,190.75 2201.8,263.55 1908.3,262.08 1198.6,255.79 604.39,229 394.76,219.55 340.81,227.87 133.39,196 127.91,195.16 122.23,\ -194.11 116.58,192.94"]; + lp="613.39,221.5", + pos="e,106.48,190.74 3122.2,263.24 2650.6,260.46 1098,249.92 599.39,229 391.95,220.3 338.6,227.61 133.39,196 127.91,195.16 122.23,194.1 \ +116.58,192.94"]; "entity to disease association mixin" [height=0.5, pos="313.39,178", width=4.7482]; "gene to disease association" -> "entity to disease association mixin" [label=uses, - lp="831.89,221.5", - pos="e,420.43,192.05 2201.6,264.35 1934.1,264.26 1325.9,260.24 815.39,229 683.2,220.91 532.03,204.93 430.42,193.21"]; + lp="823.89,221.5", + pos="e,418.23,192.27 3121.7,263.61 2674.2,262.08 1262.8,255.25 807.39,229 677.18,221.5 528.33,205.4 428.35,193.48"]; "gene to entity association mixin" [height=0.5, pos="661.39,178", width=4.4232]; "gene to disease association" -> "gene to entity association mixin" [label=uses, - lp="975.89,221.5", - pos="e,733.88,194.1 2202.5,262.98 1903,260.35 1197.4,251.87 959.39,229 886.09,221.96 803.57,207.6 743.99,196.07"]; + lp="974.89,221.5", + pos="e,732.71,194.13 3122.2,263.13 2659.3,260.01 1172.9,248.58 958.39,229 884.93,222.3 802.23,207.79 742.79,196.13"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "gene to disease association" -> id [color=blue, label=id, - lp="1097.4,221.5", - pos="e,906.37,190.01 2202.1,263.09 1923.9,260.75 1302,252.95 1090.4,229 1016.1,220.59 997.49,215.87 925.39,196 922.28,195.14 919.08,194.18 \ -915.88,193.17", + lp="1094.4,221.5", + pos="e,906.38,190 3122.1,263.26 2676.6,260.67 1288.4,250.9 1087.4,229 1014.3,221.04 996.2,215.65 925.39,196 922.29,195.14 919.09,194.17 \ +915.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "gene to disease association" -> iri [color=blue, label=iri, - lp="1218.4,221.5", - pos="e,1011,190.18 2202.6,262.35 1945.4,258.82 1398.7,249.16 1210.4,229 1130,220.39 1109.8,215.73 1031.4,196 1028,195.14 1024.4,194.17 \ -1020.9,193.16", + lp="1211.4,221.5", + pos="e,1011.3,190.23 3122.4,263.04 2693.3,259.84 1392.7,248.62 1203.4,229 1126,220.97 1106.8,215.26 1031.4,196 1028,195.14 1024.5,194.18 \ +1021,193.17", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "gene to disease association" -> name [color=blue, label=name, - lp="1333.4,221.5", - pos="e,1137.6,190.9 2203,262.43 1964.5,259.18 1481.3,250.15 1313.4,229 1255.6,221.72 1190.8,205.6 1147.3,193.62", + lp="1322.4,221.5", + pos="e,1136.2,191.27 3122,263.25 2706.6,260.76 1481.1,251.55 1302.4,229 1248,222.14 1187.1,206.21 1146,194.16", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "gene to disease association" -> description [color=blue, label=description, - lp="1459.9,221.5", - pos="e,1286.7,193.43 2202.2,262.89 1983.6,260.43 1565.8,252.7 1419.4,229 1377.1,222.15 1330.4,208.17 1296.4,196.73", + lp="1449.9,221.5", + pos="e,1284.6,193.78 3121.7,263.62 2721.6,262.2 1576.5,255.81 1409.4,229 1369.6,222.62 1326.1,208.77 1294.2,197.26", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "gene to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1614.4,221.5", - pos="e,1427,191.5 2203.7,261.65 2015.7,257.74 1685.8,248.33 1567.4,229 1522.1,221.61 1471.9,206.52 1436.9,194.84", + lp="1606.4,221.5", + pos="e,1425.7,191.88 3121.9,263.3 2744.7,261.08 1711.5,252.88 1559.4,229 1516.1,222.21 1468.4,207.12 1435.1,195.28", style=solid]; predicate [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=2.1665]; "gene to disease association" -> predicate [color=blue, label=predicate, - lp="1769.4,221.5", - pos="e,1584.4,192.89 2201.9,263.57 2078.9,261.39 1894.2,253.72 1735.4,229 1687.1,221.47 1633.3,207.23 1594.5,195.86", + lp="1765.4,221.5", + pos="e,1583.1,193.23 3122.5,262.69 2773.1,259.08 1866.7,247.99 1731.4,229 1683.7,222.31 1630.9,207.91 1592.9,196.27", style=solid]; negated [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=1.2999]; "gene to disease association" -> negated [color=blue, label=negated, - lp="1905.4,221.5", - pos="e,1718.2,190.23 2207.8,259.63 2114.8,255.19 1987.4,246.35 1876.4,229 1824.8,220.93 1766.9,204.98 1728.1,193.26", + lp="1907.4,221.5", + pos="e,1717.4,190.44 3121.7,264.11 2821.4,263.78 2115.6,259.63 1878.4,229 1825.5,222.17 1766.3,205.69 1727.2,193.51", style=solid]; qualifiers [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=2.1304]; "gene to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2035.9,221.5", - pos="e,1866.7,193.09 2218.2,256.43 2153.7,251.14 2073.3,242.54 2002.4,229 1959.3,220.77 1911.5,207.08 1876.3,196.11", + lp="2046.9,221.5", + pos="e,1866.6,193.17 3121.5,264.13 2843.4,263.73 2223.5,259.33 2013.4,229 1966.2,222.19 1913.9,207.8 1876.3,196.2", style=solid]; publications [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=1.7332]; "gene to disease association" -> publications [color=blue, label=publications, - lp="2162.4,221.5", - pos="e,2014.9,193.28 2240.4,252.47 2201.9,246.92 2157.8,239.21 2118.4,229 2086.2,220.66 2051,207.71 2024.3,197.08", + lp="2193.4,221.5", + pos="e,2017.5,192.69 3121.7,264.08 2867.2,263.49 2332.5,258.62 2149.4,229 2107,222.14 2060.3,207.66 2026.9,196.04", style=solid]; "has evidence" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=2.0943]; "gene to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2288.9,221.5", - pos="e,2168.3,194.69 2292.2,248.01 2276.2,242.33 2258.4,235.69 2242.4,229 2220.6,219.91 2196.8,208.7 2177.4,199.2", + lp="2345.9,221.5", + pos="e,2175,193.7 3121.7,263.43 2895.1,261.73 2453.2,255.08 2299.4,229 2259.8,222.29 2216.4,208.54 2184.5,197.15", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "gene to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2403.9,221.5", - pos="e,2339.4,196.18 2339.4,246.8 2339.4,235.16 2339.4,219.55 2339.4,206.24", + lp="2497.9,221.5", + pos="e,2363.3,195.57 3124.1,261.55 2906.8,257.11 2498,246.57 2433.4,229 2411.7,223.09 2389.3,211.49 2371.9,200.95", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -143,8 +143,8 @@ digraph { width=3.015]; "gene to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2597.4,221.5", - pos="e,2542.1,195.23 2406.2,249.19 2427.6,243.71 2451.3,236.88 2472.4,229 2478.7,226.64 2507.6,212.46 2533,199.8", + lp="2666.4,221.5", + pos="e,2567.7,196.01 3123.7,261.84 2928.6,258.05 2590.1,248.68 2571.4,229 2565.6,222.91 2564.6,214.28 2565.6,205.91", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -153,9 +153,8 @@ digraph { width=3.015]; "gene to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2824.9,221.5", - pos="e,2763.7,194.43 2437.4,252.26 2453.8,250.42 2470.5,248.6 2486.4,247 2579.2,237.64 2607.3,259.38 2695.4,229 2706.9,225.02 2707.5,\ -219.55 2718.4,214 2729.7,208.22 2742.2,202.83 2754.2,198.09", + lp="2874.9,221.5", + pos="e,2782.1,195.65 3121.8,263.59 2985,261.72 2792.1,254.5 2768.4,229 2760.5,220.57 2765.6,210.87 2774.4,202.27", style=solid]; timepoint [color=blue, height=0.5, @@ -164,9 +163,8 @@ digraph { width=1.5346]; "gene to disease association" -> timepoint [color=blue, label=timepoint, - lp="2988.4,221.5", - pos="e,2974.5,195.22 2434.6,251.94 2451.8,250.06 2469.6,248.31 2486.4,247 2535.7,243.15 2885.2,246.78 2931.4,229 2939.4,225.93 2954,213.79 \ -2966.8,202.25", + lp="3025.4,221.5", + pos="e,2985.7,196.29 3141.1,255.77 3073.7,249.85 3000.8,240.83 2990.4,229 2985,222.85 2983.7,214.46 2984.2,206.3", style=solid]; "original subject" [color=blue, height=0.5, @@ -175,9 +173,8 @@ digraph { width=1.0652]; "gene to disease association" -> "original subject" [color=blue, label="original subject", - lp="3103.4,221.5", - pos="e,3081.3,192.7 2434.2,251.89 2451.5,250 2469.5,248.26 2486.4,247 2546,242.56 2967.4,247 3024.4,229 3036,225.33 3037.1,220.57 3047.4,\ -214 3055.6,208.79 3064.4,203.21 3072.7,198.07", + lp="3123.4,221.5", + pos="e,3082.3,193.19 3143.5,255.19 3109.3,250.03 3078.1,241.88 3067.4,229 3059.8,219.86 3065.6,209.22 3074.6,200.11", style=solid]; "original predicate" [color=blue, height=0.5, @@ -186,9 +183,8 @@ digraph { width=1.5887]; "gene to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3244.9,221.5", - pos="e,3200.9,195.51 2433.8,251.84 2451.2,249.94 2469.4,248.21 2486.4,247 2561,241.7 3089.6,255.99 3159.4,229 3167.1,226 3181.2,214 3193.5,\ -202.51", + lp="3248.9,221.5", + pos="e,3196.6,195.19 3206.6,248.31 3198.2,243.46 3190.6,237.16 3185.4,229 3180,220.42 3183.5,211.04 3189.8,202.75", style=solid]; "original object" [color=blue, height=0.5, @@ -197,107 +193,226 @@ digraph { width=1.0652]; "gene to disease association" -> "original object" [color=blue, label="original object", - lp="3373.9,221.5", - pos="e,3328.6,196.44 2433.4,251.81 2451,249.9 2469.2,248.18 2486.4,247 2532,243.87 3271.4,254.41 3309.4,229 3317.3,223.72 3322.4,214.9 \ -3325.7,206.13", + lp="3372.9,221.5", + pos="e,3327.7,196.09 3291.5,247.44 3299.1,242.34 3306.7,236.14 3312.4,229 3317.8,222.27 3321.8,213.85 3324.6,205.85", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3464.4,178", + width=2.1304]; + "gene to disease association" -> "subject category" [color=blue, + label="subject category", + lp="3503.9,221.5", + pos="e,3456.4,195.96 3368.2,253.83 3389.3,248.54 3410.4,240.66 3428.4,229 3437.7,222.97 3445.3,213.65 3451.2,204.68", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3635.4,178", + width=2.1304]; + "gene to disease association" -> "object category" [color=blue, + label="object category", + lp="3649.9,221.5", + pos="e,3618.2,195.65 3358.6,252.47 3374.6,250.63 3391,248.76 3406.4,247 3477.9,238.86 3500.3,255.22 3567.4,229 3583,222.89 3598.3,212.23 \ +3610.4,202.32", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3768.4,178", + width=1.0652]; + "gene to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3787.9,221.5", + pos="e,3754.7,195.21 3355.8,252.07 3372.6,250.21 3390,248.43 3406.4,247 3473.6,241.12 3646.8,254.09 3709.4,229 3723.7,223.27 3737,212.63 \ +3747.4,202.63", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3864.4,178", + width=1.0652]; + "gene to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3908.4,221.5", + pos="e,3863,196.28 3354.6,251.95 3371.8,250.06 3389.6,248.31 3406.4,247 3430.8,245.09 3826.7,243.47 3846.4,229 3853.8,223.59 3858.1,214.86 \ +3860.7,206.2", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3997.4,178", + width=2.1304]; + "gene to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4066.9,221.5", + pos="e,3990.4,196.14 3354.2,251.87 3371.5,249.98 3389.5,248.25 3406.4,247 3437.2,244.72 3935.2,243.71 3962.4,229 3972.2,223.7 3979.8,\ +214.34 3985.4,205.14", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4189.4,178", + width=2.1304]; + "gene to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4256.9,221.5", + pos="e,4183.7,196.12 3353.8,251.8 3371.2,249.9 3389.4,248.19 3406.4,247 3448.1,244.1 4122.1,249.76 4158.4,229 4167.6,223.73 4174.4,214.5 \ +4179.3,205.39", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4379.4,178", + width=1.0652]; + "gene to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4429.4,221.5", + pos="e,4372.4,196.2 3353.4,251.77 3371,249.87 3389.2,248.16 3406.4,247 3458.4,243.5 4298.4,253.51 4344.4,229 4354.2,223.77 4361.9,214.42 \ +4367.5,205.2", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4538.4,178", + width=1.0652]; + "gene to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4582.4,221.5", + pos="e,4531,195.74 3353,251.78 3370.7,249.86 3389.1,248.14 3406.4,247 3436.7,245 4474.3,242.91 4501.4,229 4511.7,223.68 4519.9,214 4525.9,\ +204.57", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4689.4,178", + width=1.0652]; + "gene to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4742.4,221.5", + pos="e,4681.4,195.77 3353,251.75 3370.7,249.84 3389.1,248.12 3406.4,247 3440.9,244.76 4619.4,244.39 4650.4,229 4661.1,223.67 4669.8,213.85 \ +4676.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4860.4,178", + width=1.0652]; + "gene to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4907.9,221.5", + pos="e,4852.1,195.79 3353,251.72 3370.7,249.81 3389.1,248.11 3406.4,247 3445.6,244.49 4785.1,246.24 4820.4,229 4831.3,223.7 4840.1,213.88 \ +4846.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5004.4,178", + width=2.347]; + "gene to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5063.9,221.5", + pos="e,5001.4,196.01 3353,251.71 3370.7,249.8 3389.1,248.1 3406.4,247 3450.1,244.23 4944.7,252.81 4981.4,229 4989.5,223.71 4994.9,214.73 \ +4998.3,205.83", style=solid]; type [height=0.5, - pos="3419.4,178", + pos="5138.4,178", width=0.86659]; "gene to disease association" -> type [color=blue, label=type, - lp="3451.4,221.5", - pos="e,3429.3,195.52 2433.4,251.77 2451,249.87 2469.2,248.15 2486.4,247 2512.5,245.24 3411,247.7 3429.4,229 3435.6,222.66 3435.4,213.62 \ -3432.9,204.96", + lp="5160.4,221.5", + pos="e,5143.5,196.18 3352.6,251.73 3370.4,249.81 3389,248.1 3406.4,247 3430.4,245.49 5120.3,245.92 5137.4,229 5143.4,223.09 5145,214.52 \ +5144.6,206.13", style=solid]; category [height=0.5, - pos="3520.4,178", + pos="5239.4,178", width=1.4263]; "gene to disease association" -> category [color=blue, label=category, - lp="3524.9,221.5", - pos="e,3509.3,195.85 2433.4,251.76 2451,249.86 2469.2,248.15 2486.4,247 2541,243.35 3421.1,250.66 3471.4,229 3483.8,223.66 3494.6,213.56 \ -3503,203.83", + lp="5237.9,221.5", + pos="e,5225.8,195.46 3352.6,251.73 3370.4,249.81 3389,248.09 3406.4,247 3455.6,243.92 5134.2,246.2 5180.4,229 5195,223.57 5208.4,212.81 \ +5218.8,202.66", style=solid]; subject [height=0.5, - pos="3634.4,178", + pos="5353.4,178", width=1.2277]; "gene to disease association" -> subject [color=blue, label=subject, - lp="3617.4,221.5", - pos="e,3617.4,194.75 2433,251.78 2450.7,249.86 2469.1,248.14 2486.4,247 2545.9,243.07 3503.5,246.95 3560.4,229 3578.4,223.32 3596,211.74 \ -3609.5,201.15", + lp="5332.4,221.5", + pos="e,5335.1,194.56 3352.6,251.72 3370.4,249.8 3389,248.09 3406.4,247 3509.9,240.53 5173.8,258.08 5273.4,229 5292.8,223.32 5312.2,211.45 \ +5327,200.7", style=solid]; object [height=0.5, - pos="3677.4,91", + pos="5396.4,91", width=1.0832]; "gene to disease association" -> object [color=blue, label=object, - lp="3720.4,178", - pos="e,3690.8,108.09 2433,251.76 2450.7,249.85 2469.1,248.13 2486.4,247 2550.8,242.79 3586.9,251.28 3647.4,229 3689.9,213.36 3695.1,186.96 \ -3700.4,142 3701.2,135.38 3702.3,133.39 3700.4,127 3699.4,123.55 3697.9,120.13 3696.1,116.85", + lp="5440.4,178", + pos="e,5409.8,108.09 3352.6,251.72 3370.4,249.79 3389,248.09 3406.4,247 3460.6,243.62 5310.9,246.42 5362.4,229 5385.5,221.16 5393,216.42 \ +5406.4,196 5420,175.38 5416.5,166.51 5419.4,142 5420.2,135.38 5421.3,133.39 5419.4,127 5418.4,123.55 5416.9,120.13 5415.1,116.85", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3861.4,178", + pos="5580.4,178", width=2.3651]; "gene to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3849.4,221.5", - pos="e,3829.2,194.69 2433,251.75 2450.7,249.84 2469.1,248.12 2486.4,247 2624.1,238.06 3592.8,254.66 3728.4,229 3760.1,223 3794.1,210.08 \ -3819.8,198.88", + lp="5568.4,221.5", + pos="e,5548.2,194.74 3352.6,251.71 3370.4,249.79 3389,248.08 3406.4,247 3519.6,239.98 5335.9,249.77 5447.4,229 5479.1,223.09 5513.1,210.17 \ +5538.8,198.94", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4040.4,178", + pos="5759.4,178", width=2.1123]; "gene to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4030.4,221.5", - pos="e,4011.6,194.82 2433,251.72 2450.7,249.81 2469.1,248.11 2486.4,247 2645.5,236.83 3765.3,261.48 3921.4,229 3949.7,223.1 3979.8,210.42 \ -4002.6,199.31", + lp="5749.4,221.5", + pos="e,5730.6,194.86 3352.6,251.7 3370.4,249.78 3389,248.08 3406.4,247 3530.3,239.36 5518.8,254.01 5640.4,229 5668.8,223.17 5698.8,210.48 \ +5721.6,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4177.4,178", + pos="5896.4,178", width=1.011]; "gene to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4179.9,221.5", - pos="e,4159.5,193.83 2433,251.7 2450.7,249.79 2469.1,248.09 2486.4,247 2575.6,241.36 4009.5,253.65 4095.4,229 4115.6,223.2 4135.8,210.96 \ -4151.1,200.05", + lp="5898.9,221.5", + pos="e,5878.5,193.85 3352.6,251.69 3370.4,249.77 3389,248.07 3406.4,247 3473.2,242.9 5750.1,247.33 5814.4,229 5834.6,223.23 5854.9,211 \ +5870.1,200.07", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2533.4,265", + pos="3453.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2664.4,265", + pos="3584.4,265", width=2.0762]; subject -> object [label=relation, - lp="3672.4,134.5", - pos="e,3659.5,107.23 3635.5,159.55 3636.7,149.57 3639.2,137.07 3644.4,127 3646.6,122.68 3649.5,118.52 3652.7,114.66"]; + lp="5391.4,134.5", + pos="e,5378.5,107.23 5354.5,159.55 5355.7,149.57 5358.2,137.07 5363.4,127 5365.6,122.68 5368.5,118.52 5371.7,114.66"]; relation [height=0.5, - pos="3622.4,18", + pos="5341.4,18", width=1.2999]; - subject -> relation [pos="e,3623.7,36.188 3633.1,159.79 3631,132.48 3627,78.994 3624.5,46.38", + subject -> relation [pos="e,5342.7,36.188 5352.1,159.79 5350,132.48 5346,78.994 5343.5,46.38", style=dotted]; "gene to disease association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2867.4,265", + pos="3787.4,265", width=3.0692]; - object -> relation [pos="e,3635.2,35.54 3664.9,73.889 3658,64.939 3649.2,53.617 3641.4,43.584", + object -> relation [pos="e,5354.2,35.54 5383.9,73.889 5377,64.939 5368.2,53.617 5360.4,43.584", style=dotted]; "gene to disease association_object" [color=blue, height=0.5, label=disease, - pos="3041.4,265", + pos="3961.4,265", width=1.2638]; } diff --git a/graphviz/gene_to_disease_association.svg b/graphviz/gene_to_disease_association.svg index bc2738b239..5cfc87ff90 100644 --- a/graphviz/gene_to_disease_association.svg +++ b/graphviz/gene_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to disease association - -gene to disease association + +gene to disease association @@ -24,9 +24,9 @@ gene to disease association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to disease association->entity to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ gene to disease association->gene to entity association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ gene to disease association->id - - -id + + +id @@ -76,9 +76,9 @@ gene to disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ gene to disease association->name - - -name + + +name @@ -102,9 +102,9 @@ gene to disease association->description - - -description + + +description @@ -115,9 +115,9 @@ gene to disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ gene to disease association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ gene to disease association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ gene to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ gene to disease association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ gene to disease association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ gene to disease association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ gene to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ gene to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ gene to disease association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ gene to disease association->original subject - - -original subject + + +original subject @@ -258,9 +258,9 @@ gene to disease association->original predicate - - -original predicate + + +original predicate @@ -271,149 +271,292 @@ gene to disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to disease association->object category + + +object category + + + +subject closure + +string + + + +gene to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to disease association->type - - -type + + +type - + category - -category + +category - + gene to disease association->category - - -category + + +category - + subject - -subject + +subject - + gene to disease association->subject - - -subject + + +subject - + object - -object + +object - + gene to disease association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + gene to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + gene to disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + gene to disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to disease association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene to disease association_object - -disease + +disease diff --git a/graphviz/gene_to_expression_site_association.gv b/graphviz/gene_to_expression_site_association.gv index dc4f1e4a71..795a017087 100644 --- a/graphviz/gene_to_expression_site_association.gv +++ b/graphviz/gene_to_expression_site_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3402,283"]; + graph [bb="0,0,5125,283"]; node [label="\N"]; "gene to expression site association" [height=0.5, label="gene to expression site association", - pos="1748.4,265", + pos="2594.4,265", width=4.8024]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to expression site association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.13,191.69 1575.3,264.59 1240.5,264.95 515.2,261.76 267.39,229 213.88,221.93 154.05,206.43 112.91,194.55"]; + lp="280.39,221.5", + pos="e,102.91,191.8 2421.7,263.65 1918.8,262.31 477.63,256.12 266.39,229 213.1,222.16 153.57,206.63 112.64,194.68"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to expression site association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 1576.1,263.32 1263.7,261.45 615.6,254.53 391.39,229 318.39,220.69 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="395.39,221.5", + pos="e,210.38,189.98 2422.2,263.14 1938.2,260.46 587.79,251.07 388.39,229 316.66,221.06 298.9,215.43 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to expression site association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 1576.9,262.58 1286.3,259.61 709.27,251.07 507.39,229 430.02,220.54 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="508.39,221.5", + pos="e,315.3,190.19 2422.7,262.91 1956.3,259.71 688.61,249.23 500.39,229 426.04,221.01 407.78,214.78 335.39,196 332.02,195.12 328.54,\ +194.16 325.06,193.14", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to expression site association" -> name [color=blue, label=name, - lp="617.39,221.5", - pos="e,439.57,191.41 1576.1,263.36 1302.5,261.57 780.96,254.77 597.39,229 545.94,221.78 488.49,206.2 449.16,194.34", + lp="615.39,221.5", + pos="e,439.15,191.55 2421.9,263.3 1969.8,261.13 773.33,253.15 595.39,229 544.62,222.11 488.03,206.59 449.14,194.65", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to expression site association" -> description [color=blue, label=description, - lp="739.89,221.5", - pos="e,586.21,194 1575.4,264.34 1322,263.79 862.21,258.56 699.39,229 663.55,222.49 624.58,209.05 595.63,197.74", + lp="735.89,221.5", + pos="e,585.2,194.16 2421.7,263.92 1985.6,263.28 862.22,258.72 695.39,229 660.55,222.79 622.82,209.43 594.72,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,7 +61,7 @@ digraph { "gene to expression site association" -> "has attribute" [color=blue, label="has attribute", lp="881.39,221.5", - pos="e,726.05,192.79 1575.6,263.73 1351,262.27 971.35,255.76 834.39,229 799.98,222.28 762.69,208.34 735.56,196.88", + pos="e,726.02,192.95 2421.6,263.77 2008.6,262.77 987.21,257.4 834.39,229 799.92,222.59 762.64,208.63 735.52,197.08", style=solid]; negated [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { "gene to expression site association" -> negated [color=blue, label=negated, lp="1036.4,221.5", - pos="e,847.62,190.31 1582.7,259.76 1398.9,254.42 1114.3,244.08 1007.4,229 955.07,221.62 896.53,205.39 857.57,193.41", + pos="e,847.23,190.47 2421.3,264.79 2068.3,265.64 1276.1,263.47 1007.4,229 954.82,222.26 896.1,205.83 857.18,193.63", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to expression site association" -> qualifiers [color=blue, label=qualifiers, - lp="1166.9,221.5", - pos="e,995.77,193.3 1575.6,264.08 1451.8,261.73 1281.4,253.58 1133.4,229 1089.5,221.7 1040.9,207.74 1005.4,196.42", + lp="1175.9,221.5", + pos="e,996.36,193.22 2423.6,262.14 2067,257.94 1266,246.67 1142.4,229 1095.4,222.29 1043.4,207.89 1006,196.26", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to expression site association" -> publications [color=blue, label=publications, - lp="1300.4,221.5", - pos="e,1144.7,193.27 1576.7,262.74 1481.5,259.31 1361.5,250.47 1256.4,229 1221.2,221.8 1182.7,208.28 1154.3,197.11", + lp="1322.4,221.5", + pos="e,1147.2,192.74 2423.9,261.98 2093.5,257.69 1388.3,246.6 1278.4,229 1236.2,222.25 1189.8,207.76 1156.7,196.1", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "gene to expression site association" -> "has evidence" [color=blue, label="has evidence", - lp="1440.9,221.5", - pos="e,1299.2,194.38 1590,257.71 1528.3,252.83 1457.4,244.21 1394.4,229 1364.8,221.86 1332.9,209.3 1308.5,198.55", + lp="1482.9,221.5", + pos="e,1306,193.53 2421.5,264.22 2146.2,263.64 1620.7,258.53 1436.4,229 1394.7,222.32 1348.9,208.33 1315.5,196.84", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "gene to expression site association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1571.9,221.5", - pos="e,1477.9,196.21 1615.1,253.52 1570.1,248.11 1526.4,240.22 1507.4,229 1497.6,223.21 1489.4,213.81 1483.2,204.71", + lp="1639.9,221.5", + pos="e,1496.6,195.62 2423.8,261.9 2155,258.03 1655.2,248.33 1575.4,229 1551,223.09 1525.5,211.25 1505.6,200.58", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "gene to expression site association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1738.4,221.5", - pos="e,1663.3,194.83 1667.3,249.01 1657.9,244.08 1649.6,237.57 1643.4,229 1635.5,218.08 1642.7,208.17 1654.5,200.11", + lp="1813.4,221.5", + pos="e,1704.4,196.16 2423.4,262.29 2176.3,259.09 1745.5,250.46 1718.4,229 1711.4,223.46 1707.7,214.7 1705.8,206.06", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -130,9 +130,8 @@ digraph { width=3.015]; "gene to expression site association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1962.9,221.5", - pos="e,1898.2,194.67 1792.8,247.55 1806.1,242.14 1820.5,235.76 1833.4,229 1844.2,223.32 1845.6,219.73 1856.4,214 1866.6,208.55 1877.9,\ -203.32 1888.8,198.64", + lp="2022.9,221.5", + pos="e,1922.7,195.92 2425.5,261.03 2230.4,256.75 1933.7,247.27 1916.4,229 1909.8,222.04 1911.9,212.84 1916.9,204.23", style=solid]; timepoint [color=blue, height=0.5, @@ -141,8 +140,8 @@ digraph { width=1.5346]; "gene to expression site association" -> timepoint [color=blue, label=timepoint, - lp="2126.4,221.5", - pos="e,2108.8,195.92 1871.9,252.39 1958.4,243.96 2060.2,233.3 2069.4,229 2081.8,223.2 2093.1,213.23 2102,203.71", + lp="2180.4,221.5", + pos="e,2125,196.29 2430.9,259.14 2312.4,254.29 2169,245.17 2145.4,229 2137.4,223.54 2132,214.69 2128.4,205.94", style=solid]; "original subject" [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.0652]; "gene to expression site association" -> "original subject" [color=blue, label="original subject", - lp="2240.4,221.5", - pos="e,2213.2,193.59 1871.2,252.26 1891,250.45 1911.3,248.64 1930.4,247 1981.9,242.6 2113.7,246.51 2162.4,229 2164.9,228.1 2186.3,212.95 \ -2204.9,199.56", + lp="2280.4,221.5", + pos="e,2224,195.81 2432.6,258.64 2339.8,253.84 2239,245 2224.4,229 2218.6,222.62 2218.5,213.83 2220.7,205.39", style=solid]; "original predicate" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.5887]; "gene to expression site association" -> "original predicate" [color=blue, label="original predicate", - lp="2381.9,221.5", - pos="e,2336,195.71 1868.7,252 1889.3,250.17 1910.5,248.42 1930.4,247 1971.1,244.1 2260.1,245.54 2297.4,229 2309.8,223.48 2320.9,213.36 \ -2329.4,203.65", + lp="2408.9,221.5", + pos="e,2341.3,196.26 2435,257.97 2394.4,252.94 2358.6,244.16 2345.4,229 2340,222.82 2338.9,214.42 2339.6,206.27", style=solid]; "original object" [color=blue, height=0.5, @@ -173,116 +170,233 @@ digraph { width=1.0652]; "gene to expression site association" -> "original object" [color=blue, label="original object", - lp="2509.9,221.5", - pos="e,2461.4,196.18 1867.3,251.89 1888.3,250.04 1910,248.31 1930.4,247 1959.1,245.16 2424.8,246.76 2447.4,229 2454.4,223.47 2458.1,214.72 \ -2460,206.08", + lp="2538.9,221.5", + pos="e,2466.5,195.98 2521.3,248.57 2509.1,243.72 2497.2,237.35 2487.4,229 2480,222.74 2474.5,213.87 2470.4,205.33", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "gene to expression site association" -> "subject category" [color=blue, + label="subject category", + lp="2653.9,221.5", + pos="e,2594.4,196.18 2594.4,246.8 2594.4,235.16 2594.4,219.55 2594.4,206.24", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "gene to expression site association" -> "object category" [color=blue, + label="object category", + lp="2788.9,221.5", + pos="e,2751.9,196.04 2668.2,248.68 2684,243.72 2700.3,237.28 2714.4,229 2725.8,222.34 2736.5,212.6 2745.1,203.48", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "gene to expression site association" -> "subject closure" [color=blue, + label="subject closure", + lp="2923.9,221.5", + pos="e,2886.8,195.3 2727,253.43 2776.7,247.85 2826.5,239.87 2848.4,229 2860.6,222.94 2871.6,212.74 2880.2,203.13", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "gene to expression site association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2996.9,196.12 2718.2,252.35 2737.7,250.54 2757.6,248.71 2776.4,247 2821.7,242.88 2944.3,256.78 2980.4,229 2987.6,223.41 2992,214.65 \ +2994.6,206.01", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "gene to expression site association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3199.9,221.5", + pos="e,3124.3,196.05 2715.2,252.08 2735.6,250.25 2756.6,248.48 2776.4,247 2811.9,244.34 3065.3,246.33 3096.4,229 3106.1,223.59 3113.7,\ +214.2 3119.4,205.02", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "gene to expression site association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.4,196.09 2713.3,251.89 2734.3,250.04 2756,248.31 2776.4,247 2805,245.17 3266.5,243.18 3291.4,229 3300.8,223.64 3307.9,214.27 \ +3312.9,205.07", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "gene to expression site association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.17 2712.3,251.82 2733.6,249.95 2755.6,248.23 2776.4,247 2815.3,244.68 3444,247.46 3478.4,229 3488.2,223.74 3495.8,214.38 \ +3501.5,205.17", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "gene to expression site association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.72 2711.8,251.78 2733.3,249.9 2755.5,248.19 2776.4,247 2824,244.28 3593,250.93 3635.4,229 3645.7,223.66 3653.9,213.98 \ +3659.9,204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "gene to expression site association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.76 2711.8,251.73 2733.3,249.85 2755.5,248.16 2776.4,247 2832.3,243.89 3734.3,254.02 3784.4,229 3795.1,223.65 3803.7,\ +213.83 3810.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "gene to expression site association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.78 2711.3,251.73 2732.9,249.84 2755.3,248.14 2776.4,247 2809.1,245.23 3925,243.4 3954.4,229 3965.2,223.68 3974.1,213.86 \ +3980.7,204.32", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4138.4,178", + width=2.347]; + "gene to expression site association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4197.9,221.5", + pos="e,4135.4,196 2711.3,251.69 2732.9,249.81 2755.3,248.12 2776.4,247 2813.5,245.02 4084.2,249.28 4115.4,229 4123.5,223.7 4128.8,214.72 \ +4132.3,205.82", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4272.4,178", width=0.86659]; "gene to expression site association" -> type [color=blue, label=type, - lp="2586.4,221.5", - pos="e,2561.8,194.86 1866.8,251.82 1887.9,249.96 1909.8,248.25 1930.4,247 1948,245.93 2553.1,241.65 2565.4,229 2572,222.21 2570.6,212.69 \ -2566.6,203.78", + lp="4294.4,221.5", + pos="e,4277.5,196.18 2711.3,251.67 2732.9,249.79 2755.3,248.11 2776.4,247 2797.1,245.91 4256.7,243.62 4271.4,229 4277.4,223.09 4279,214.51 \ +4278.6,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4373.4,178", width=1.4263]; "gene to expression site association" -> category [color=blue, label=category, - lp="2656.9,221.5", - pos="e,2640.8,195.77 1866.8,251.79 1887.9,249.94 1909.8,248.23 1930.4,247 1967.9,244.75 2572.4,244.93 2606.4,229 2617.9,223.62 2627.6,\ -213.65 2635,204.02", + lp="4371.9,221.5", + pos="e,4359.8,195.45 2711.3,251.66 2732.9,249.78 2755.3,248.11 2776.4,247 2819.1,244.76 4274.4,243.95 4314.4,229 4329,223.56 4342.4,212.8 \ +4352.8,202.65", style=solid]; "stage qualifier" [height=0.5, - pos="2797.4,178", + pos="4520.4,178", width=2.1484]; "gene to expression site association" -> "stage qualifier" [color=blue, label="stage qualifier", - lp="2785.9,221.5", - pos="e,2771.4,195.22 1866.3,251.78 1887.6,249.92 1909.6,248.21 1930.4,247 2014.9,242.06 2610,248.64 2692.4,229 2717,223.14 2742.6,211.06 \ -2762.4,200.24", + lp="4503.9,221.5", + pos="e,4492.7,195.08 2711.3,251.65 2732.9,249.77 2755.3,248.1 2776.4,247 2866.9,242.28 4318.8,248.23 4407.4,229 4434.1,223.21 4462.1,\ +210.83 4483.6,199.84", style=solid]; "quantifier qualifier" [height=0.5, - pos="2990.4,178", + pos="4713.4,178", width=2.7081]; "gene to expression site association" -> "quantifier qualifier" [color=blue, label="quantifier qualifier", - lp="2967.4,221.5", - pos="e,2953.9,194.75 1865.8,251.76 1887.3,249.88 1909.5,248.18 1930.4,247 2031.5,241.29 2741.6,246.3 2841.4,229 2876.9,222.84 2915.4,\ -209.73 2944.4,198.48", + lp="4687.4,221.5", + pos="e,4675.9,194.73 2710.8,251.68 2732.6,249.78 2755.2,248.1 2776.4,247 2974.3,236.78 4363.9,260.96 4559.4,229 4596.3,222.96 4636.5,\ +209.69 4666.5,198.33", style=solid]; subject [height=0.5, - pos="3150.4,178", + pos="4873.4,178", width=1.2277]; "gene to expression site association" -> subject [color=blue, label=subject, - lp="3109.4,221.5", - pos="e,3126,193.35 1865.8,251.7 1887.3,249.83 1909.5,248.14 1930.4,247 2053.3,240.27 2918.2,255.64 3038.4,229 3066.1,222.86 3095.3,209.56 \ -3117,198.22", + lp="4830.4,221.5", + pos="e,4848.8,193.17 2710.8,251.66 2732.6,249.77 2755.2,248.09 2776.4,247 2886.4,241.37 4650.7,251.91 4758.4,229 4787.1,222.9 4817.4,\ +209.36 4839.7,197.92", style=solid]; object [height=0.5, - pos="3193.4,91", + pos="4916.4,91", width=1.0832]; "gene to expression site association" -> object [color=blue, label=object, - lp="3243.4,178", - pos="e,3206.8,108.09 1865.3,251.72 1886.9,249.83 1909.3,248.14 1930.4,247 1997.5,243.37 3074.2,245.32 3139.4,229 3170.4,221.22 3183.6,\ -221.17 3203.4,196 3222.7,171.45 3225.3,156.9 3216.4,127 3215.4,123.55 3213.9,120.13 3212.1,116.85", + lp="4966.4,178", + pos="e,4929.8,108.09 2710.8,251.65 2732.6,249.76 2755.2,248.08 2776.4,247 2892,241.11 4747.8,256.09 4860.4,229 4892.3,221.33 4906,221.67 \ +4926.4,196 4945.8,171.57 4948.3,156.9 4939.4,127 4938.4,123.55 4936.9,120.13 4935.1,116.85", style=solid]; predicate [height=0.5, - pos="3347.4,178", + pos="5070.4,178", width=1.5165]; "gene to expression site association" -> predicate [color=blue, label=predicate, - lp="3320.4,221.5", - pos="e,3323.6,194.32 1865.3,251.7 1886.9,249.82 1909.3,248.13 1930.4,247 2003.3,243.1 3173.4,245.84 3244.4,229 3269.3,223.1 3295.2,210.51 \ -3314.7,199.43", + lp="5043.4,221.5", + pos="e,5046.6,194.36 2710.8,251.64 2732.6,249.75 2755.2,248.08 2776.4,247 2898,240.83 4848.9,256.76 4967.4,229 4992.3,223.17 5018.2,210.57 \ +5037.8,199.49", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1977.4,265", + pos="2823.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2108.4,265", + pos="2954.4,265", width=2.0762]; "gene to expression site association_stage qualifier" [color=blue, height=0.5, label="life stage", - pos="2255.4,265", + pos="3101.4,265", width=1.4985]; "gene to expression site association_quantifier qualifier" [color=blue, height=0.5, label="ontology class", - pos="2404.4,265", + pos="3250.4,265", width=2.1304]; subject -> object [label=relation, - lp="3188.4,134.5", - pos="e,3175.5,107.23 3151.5,159.55 3152.7,149.57 3155.2,137.07 3160.4,127 3162.6,122.68 3165.5,118.52 3168.7,114.66"]; + lp="4911.4,134.5", + pos="e,4898.5,107.23 4874.5,159.55 4875.7,149.57 4878.2,137.07 4883.4,127 4885.6,122.68 4888.5,118.52 4891.7,114.66"]; relation [height=0.5, - pos="3138.4,18", + pos="4861.4,18", width=1.2999]; - subject -> relation [pos="e,3139.7,36.188 3149.1,159.79 3147,132.48 3143,78.994 3140.5,46.38", + subject -> relation [pos="e,4862.7,36.188 4872.1,159.79 4870,132.48 4866,78.994 4863.5,46.38", style=dotted]; "gene to expression site association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2609.4,265", + pos="3455.4,265", width=3.0692]; - object -> relation [pos="e,3151.2,35.54 3180.9,73.889 3174,64.939 3165.2,53.617 3157.4,43.584", + object -> relation [pos="e,4874.2,35.54 4903.9,73.889 4897,64.939 4888.2,53.617 4880.4,43.584", style=dotted]; "gene to expression site association_object" [color=blue, height=0.5, label="anatomical entity", - pos="2829.4,265", + pos="3675.4,265", width=2.5456]; "gene to expression site association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3017.4,265", + pos="3863.4,265", width=2.1665]; } diff --git a/graphviz/gene_to_expression_site_association.svg b/graphviz/gene_to_expression_site_association.svg index 6bda07a5e6..fb508d8871 100644 --- a/graphviz/gene_to_expression_site_association.svg +++ b/graphviz/gene_to_expression_site_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to expression site association - -gene to expression site association + +gene to expression site association @@ -24,9 +24,9 @@ gene to expression site association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to expression site association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to expression site association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to expression site association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to expression site association->description - - -description + + +description @@ -89,8 +89,8 @@ gene to expression site association->has attribute - - + + has attribute @@ -102,8 +102,8 @@ gene to expression site association->negated - - + + negated @@ -115,9 +115,9 @@ gene to expression site association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to expression site association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ gene to expression site association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ gene to expression site association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ gene to expression site association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ gene to expression site association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ gene to expression site association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ gene to expression site association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ gene to expression site association->original predicate - - -original predicate + + +original predicate @@ -232,167 +232,310 @@ gene to expression site association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to expression site association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to expression site association->object category + + +object category + + + +subject closure + +string + + + +gene to expression site association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to expression site association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to expression site association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to expression site association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to expression site association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to expression site association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to expression site association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to expression site association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to expression site association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to expression site association->type - - -type + + +type - + category - -category + +category - + gene to expression site association->category - - -category + + +category - + stage qualifier - -stage qualifier + +stage qualifier - + gene to expression site association->stage qualifier - - -stage qualifier + + +stage qualifier - + quantifier qualifier - -quantifier qualifier + +quantifier qualifier - + gene to expression site association->quantifier qualifier - - -quantifier qualifier + + +quantifier qualifier - + subject - -subject + +subject - + gene to expression site association->subject - - -subject + + +subject - + object - -object + +object - + gene to expression site association->object - - -object + + +object - + predicate - -predicate + +predicate - + gene to expression site association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + gene to expression site association_stage qualifier - -life stage + +life stage - + gene to expression site association_quantifier qualifier - -ontology class + +ontology class - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to expression site association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene to expression site association_object - -anatomical entity + +anatomical entity - + gene to expression site association_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_gene_association.gv b/graphviz/gene_to_gene_association.gv index e19fa890ab..bc6e45e42b 100644 --- a/graphviz/gene_to_gene_association.gv +++ b/graphviz/gene_to_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "gene to gene association" [height=0.5, label="gene to gene association", - pos="1542.4,265", + pos="2492.4,265", width=3.4844]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to gene association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1417,263.89 1141,263.11 488.35,258.13 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2366.9,263.66 1927.8,262.26 475.16,255.63 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to gene association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1417.4,262.78 1162.6,259.87 590.84,251.03 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,\ -194.16 219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2367.4,263.26 1945.2,260.58 587,250.37 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1418.5,261.98 1185.4,257.82 690.03,247.13 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,\ -194.19 324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2367.7,263.05 1961.3,259.78 691.29,248.12 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ +194.18 325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1418.4,262.08 1202.9,258.29 767.68,248.45 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2367.4,263.22 1974.6,260.57 780.63,250.77 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1418,262.4 1222.4,259.25 851.58,250.59 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2367.3,263.53 1989.6,261.84 876.9,254.7 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1419.7,261.02 1254.9,256.44 970.86,246.31 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2367.3,263.21 2012,260.7 1012.8,251.69 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "gene to gene association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1418.7,261.98 1315.4,258.75 1164.5,250.4 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2366.9,264.61 2063.1,265.48 1294.7,264.05 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "gene to gene association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1427.6,257.72 1354.2,252.58 1257.3,243.7 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2367.2,263.68 2086.9,262.46 1416.2,256.66 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "gene to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1442.1,254.18 1394.8,248.55 1337.9,240.31 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2366.8,263.74 2107.7,262.64 1521.5,257.02 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "gene to gene association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1471.2,250.16 1446.6,244.59 1419,237.46 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2367,263.72 2130.6,262.53 1627.2,256.71 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "gene to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461,195.47 1522.4,247.21 1507.1,234.32 1485.8,216.38 1468.9,202.13", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2367.4,262.98 2158.9,260.62 1748.9,253 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "gene to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.2,247.31 1578.6,241.84 1587.6,235.49 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2366.8,264.76 2183.7,264.74 1853.1,260.17 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "gene to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1631.2,252.27 1666.7,246.62 1707.8,238.9 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2369.6,261.29 2195,256.82 1894,246.6 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "gene to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.8,195.23 1630.2,252.09 1645.9,250.2 1662.1,248.41 1677.4,247 1813.1,234.48 1850.2,257.79 1983.4,229 2013.5,222.5 2045.8,210.11 \ -2070.6,199.29", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2368.7,261.98 2252.7,258.76 2094.1,250.46 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "gene to gene association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.78 1628.7,251.91 1644.8,249.99 1661.6,248.24 1677.4,247 1740.7,242.03 2190.5,255.11 2248.4,229 2260.4,223.56 2270.9,\ -213.45 2278.8,203.73", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2382.6,256.23 2345,251.15 2309.4,242.78 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "gene to gene association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.23 1628.7,251.85 1644.8,249.94 1661.6,248.2 1677.4,247 1751.1,241.38 2272.7,253.75 2342.4,229 2351.2,225.86 2368.2,\ -212.73 2382.5,200.72", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2404.6,252.07 2392.8,246.78 2382.1,239.36 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,203 @@ digraph { width=1.5887]; "gene to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.25 1628.3,251.84 1644.6,249.91 1661.5,248.18 1677.4,247 1722,243.7 2441.3,248.8 2481.4,229 2492.1,223.72 2500.8,214.09 \ -2507.4,204.69", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "gene to gene association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.98 1628,251.83 1644.3,249.9 1661.4,248.16 1677.4,247 1703.8,245.09 2608.2,243.49 2630.4,229 2638.5,223.68 2643.8,214.69 \ -2647.3,205.79", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2581.6,252.21 2595.9,246.98 2609.6,239.54 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "gene to gene association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2581.2,252.19 2649.9,242.92 2734,231.21 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "gene to gene association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.7,195.63 2580.9,252.17 2596.4,250.3 2612.3,248.49 2627.4,247 2682.4,241.55 2823.8,248.87 2875.4,229 2890.4,223.21 2904.8,\ +212.62 2916.1,202.68", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "gene to gene association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.26 2579.4,252.01 2595.4,250.11 2611.9,248.34 2627.4,247 2670.5,243.29 2976.3,245.35 3016.4,229 3030.2,223.35 3042.9,\ +212.72 3052.7,202.71", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "gene to gene association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.35 2579.1,251.9 2595.1,250 2611.7,248.25 2627.4,247 2656.5,244.67 3128.5,245.77 3152.4,229 3160.1,223.61 3164.8,214.78 \ +3167.7,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "gene to gene association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.19 2578.7,251.87 2594.8,249.95 2611.6,248.21 2627.4,247 2662.9,244.27 3236.8,245.48 3268.4,229 3278.6,223.7 3286.6,\ +214.21 3292.6,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "gene to gene association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.16 2578.3,251.82 2594.6,249.9 2611.5,248.17 2627.4,247 2673.8,243.59 3423.7,251.48 3464.4,229 3474,223.72 3481.2,214.36 \ +3486.5,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "gene to gene association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2578,251.82 2594.3,249.88 2611.4,248.15 2627.4,247 2684.1,242.94 3601,255.38 3651.4,229 3661.6,223.66 3669.6,213.98 \ +3675.4,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "gene to gene association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.76 2578,251.79 2594.3,249.86 2611.4,248.13 2627.4,247 2660.1,244.7 3779.1,243.8 3808.4,229 3818.9,223.71 3827.2,214.03 \ +3833.4,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "gene to gene association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.78 2578,251.76 2594.3,249.84 2611.4,248.11 2627.4,247 2664.3,244.44 3925.3,245.45 3958.4,229 3969.1,223.68 3977.8,213.86 \ +3984.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "gene to gene association" -> "object label closure" [color=blue, + label="object label closure", + lp="4216.9,221.5", + pos="e,4160.1,195.8 2577.6,251.79 2594.1,249.84 2611.3,248.11 2627.4,247 2669,244.14 4090.9,247.29 4128.4,229 4139.3,223.7 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "gene to gene association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.8,196.3 2577.6,251.77 2594.1,249.83 2611.3,248.1 2627.4,247 2673.5,243.86 4248.9,249.24 4290.4,229 4301.1,223.78 4309.9,214.17 \ +4316.4,204.75", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "gene to gene association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1628,251.81 1644.3,249.87 1661.4,248.14 1677.4,247 1707.1,244.88 2729.5,250.25 2750.4,229 2756.6,222.69 2756.6,213.66 \ -2754.2,205", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2577.6,251.76 2594.1,249.82 2611.2,248.09 2627.4,247 2652.7,245.29 4432.6,244.79 4452.4,229 4459.2,223.54 4462.6,\ +214.93 4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "gene to gene association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.87 1628,251.8 1644.3,249.87 1661.4,248.13 1677.4,247 1739.2,242.62 2735.4,253.17 2792.4,229 2804.9,223.69 2816,213.59 \ -2824.5,203.85", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2577.6,251.76 2594.1,249.81 2611.2,248.09 2627.4,247 2679.3,243.5 4449.1,245.61 4498.4,229 4514.6,223.53 4530.1,\ +212.51 4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "gene to gene association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.76 1628,251.78 1644.3,249.85 1661.4,248.13 1677.4,247 1744.2,242.31 2818.5,249.08 2882.4,229 2900.4,223.34 2918,211.76 \ -2931.5,201.16", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2577.6,251.75 2594.1,249.81 2611.2,248.09 2627.4,247 2736.4,239.66 4489.1,258.2 4594.4,229 4615.1,223.25 4636,211.09 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "gene to gene association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1628,251.77 1644.3,249.84 1661.4,248.12 1677.4,247 1749,242.01 2902,253.74 2969.4,229 3011.9,213.4 3017.1,186.96 \ -3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2577.6,251.74 2594.1,249.8 2611.2,248.08 2627.4,247 2684.4,243.17 4631,246.46 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1724.4,265", + pos="2674.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1855.4,265", + pos="2805.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "gene to gene association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2058.4,265", + pos="3008.4,265", width=3.0692]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "gene to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="2297.4,265", + pos="3247.4,265", width=3.0692]; } diff --git a/graphviz/gene_to_gene_association.svg b/graphviz/gene_to_gene_association.svg index 82ca341447..ff3af7c11c 100644 --- a/graphviz/gene_to_gene_association.svg +++ b/graphviz/gene_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene association - -gene to gene association + +gene to gene association @@ -24,9 +24,9 @@ gene to gene association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to gene association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to gene association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ gene to gene association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ gene to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ gene to gene association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ gene to gene association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ gene to gene association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ gene to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ gene to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ gene to gene association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ gene to gene association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ gene to gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to gene association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to gene association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to gene association->object category + + +object category + + + +subject closure + +string + + + +gene to gene association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to gene association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to gene association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to gene association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to gene association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to gene association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to gene association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to gene association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to gene association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to gene association->type - - -type + + +type - + category - -category + +category - + gene to gene association->category - - -category + + +category - + subject - -subject + +subject - + gene to gene association->subject - - -subject + + +subject - + object - -object + +object - + gene to gene association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to gene association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene to gene association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/gene_to_gene_coexpression_association.gv b/graphviz/gene_to_gene_coexpression_association.gv index 1517c68b2e..314949b9bd 100644 --- a/graphviz/gene_to_gene_coexpression_association.gv +++ b/graphviz/gene_to_gene_coexpression_association.gv @@ -1,22 +1,22 @@ digraph { - graph [bb="0,0,4245.3,283"]; + graph [bb="0,0,5965.3,283"]; node [label="\N"]; "gene to gene coexpression association" [height=0.5, label="gene to gene coexpression association", - pos="2228.4,265", + pos="3038.4,265", width=5.2356]; "gene to gene association" [height=0.5, pos="125.44,178", width=3.4844]; "gene to gene coexpression association" -> "gene to gene association" [label=is_a, lp="519.44,221.5", - pos="e,204.51,192 2041.1,262.81 1658.5,259.95 798.84,251.21 505.44,229 405.43,221.43 291.45,205.44 214.62,193.57"]; + pos="e,204.13,192.09 2850.1,264.26 2343.7,264.49 960.81,261.99 505.44,229 405.24,221.74 291.07,205.65 214.25,193.68"]; "gene expression mixin" [height=0.5, pos="383.44,178", width=3.1955]; "gene to gene coexpression association" -> "gene expression mixin" [label=uses, lp="650.94,221.5", - pos="e,441.57,193.58 2040.2,263.99 1679.1,263.29 901.34,258.29 634.44,229 571.81,222.13 501.55,207.53 451.34,195.87"]; + pos="e,441.05,193.59 2850.8,263.24 2323.4,260.81 851.84,252.04 634.44,229 571.58,222.34 501.07,207.64 450.82,195.89"]; id [color=blue, height=0.5, label=string, @@ -24,9 +24,9 @@ digraph { width=1.0652]; "gene to gene coexpression association" -> id [color=blue, label=id, - lp="769.44,221.5", - pos="e,583.43,189.98 2040.3,263.71 1702.1,262.49 1004.2,256.59 762.44,229 690.3,220.77 672.38,215.5 602.44,196 599.33,195.13 596.13,194.17 \ -592.93,193.15", + lp="768.44,221.5", + pos="e,583.43,189.98 2850.8,263.16 2342.9,260.58 965.91,251.58 761.44,229 689.7,221.08 671.95,215.43 602.44,196 599.33,195.13 596.13,\ +194.17 592.94,193.15", style=solid]; iri [color=blue, height=0.5, @@ -35,9 +35,9 @@ digraph { width=1.2277]; "gene to gene coexpression association" -> iri [color=blue, label=iri, - lp="882.44,221.5", - pos="e,688.35,190.2 2041,263.1 1723.9,260.92 1094.6,253.54 874.44,229 799.68,220.66 781.26,214.85 708.44,196 705.06,195.13 701.58,194.16 \ -698.1,193.15", + lp="881.44,221.5", + pos="e,688.35,190.19 2850.8,262.91 2360.7,259.8 1066.7,249.71 873.44,229 799.08,221.03 780.83,214.78 708.44,196 705.06,195.12 701.59,\ +194.16 698.1,193.14", style=solid]; name [color=blue, height=0.5, @@ -46,8 +46,8 @@ digraph { width=1.5707]; "gene to gene coexpression association" -> name [color=blue, label=name, - lp="989.44,221.5", - pos="e,812.41,191.44 2040.3,263.9 1741.1,262.87 1170.3,257.12 969.44,229 918.34,221.84 861.32,206.31 822.2,194.44", + lp="988.44,221.5", + pos="e,812.19,191.56 2850.4,263.35 2375.2,261.33 1151.5,253.78 968.44,229 917.66,222.12 861.07,206.6 822.18,194.66", style=solid]; description [color=blue, height=0.5, @@ -56,8 +56,8 @@ digraph { width=2.0943]; "gene to gene coexpression association" -> description [color=blue, label=description, - lp="1109.9,221.5", - pos="e,958.8,194.16 2043.5,261.47 1740.5,256.86 1162.2,245.99 1069.4,229 1034.5,222.61 996.66,209.32 968.39,198.05", + lp="1108.9,221.5", + pos="e,958.24,194.16 2850.1,264.04 2391.3,263.64 1240.4,259.57 1068.4,229 1033.6,222.8 995.86,209.44 967.76,198.08", style=solid]; "has attribute" [color=blue, height=0.5, @@ -66,8 +66,8 @@ digraph { width=1.4443]; "gene to gene coexpression association" -> "has attribute" [color=blue, label="has attribute", - lp="1255.4,221.5", - pos="e,1099.3,192.82 2039.9,264.51 1789.9,263.98 1362.2,258.54 1208.4,229 1173.6,222.31 1135.9,208.27 1108.5,196.77", + lp="1254.4,221.5", + pos="e,1099.1,192.96 2850.3,263.89 2415.4,263.15 1365.4,258.29 1207.4,229 1173,222.61 1135.7,208.64 1108.6,197.09", style=solid]; negated [color=blue, height=0.5, @@ -76,8 +76,8 @@ digraph { width=1.2999]; "gene to gene coexpression association" -> negated [color=blue, label=negated, - lp="1411.4,221.5", - pos="e,1221,190.38 2045.8,260.47 1836.2,255.71 1505.8,245.83 1382.4,229 1329.4,221.76 1269.9,205.39 1230.6,193.34", + lp="1409.4,221.5", + pos="e,1220.3,190.48 2851.9,262.29 2449.1,258.28 1522.8,247.19 1380.4,229 1327.9,222.28 1269.1,205.85 1230.2,193.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -86,8 +86,8 @@ digraph { width=2.1304]; "gene to gene coexpression association" -> qualifiers [color=blue, label=qualifiers, - lp="1543.9,221.5", - pos="e,1369,193.16 2048.3,259.7 1870.1,254.63 1610,244.84 1510.4,229 1465.2,221.81 1415.2,207.7 1378.9,196.3", + lp="1548.9,221.5", + pos="e,1369.4,193.23 2852.2,262.19 2474.7,258.16 1644.2,247.34 1515.4,229 1468.5,222.31 1416.5,207.91 1379.1,196.28", style=solid]; publications [color=blue, height=0.5, @@ -96,8 +96,8 @@ digraph { width=1.7332]; "gene to gene coexpression association" -> publications [color=blue, label=publications, - lp="1679.4,221.5", - pos="e,1518.5,193.14 2051.7,258.64 1906.4,253.29 1712.3,243.73 1635.4,229 1598.4,221.9 1557.9,208.15 1528.2,196.86", + lp="1695.4,221.5", + pos="e,1520.3,192.76 2852.4,262.05 2501.5,257.97 1766.6,247.36 1651.4,229 1609.3,222.28 1562.9,207.78 1529.7,196.12", style=solid]; "has evidence" [color=blue, height=0.5, @@ -106,8 +106,8 @@ digraph { width=2.0943]; "gene to gene coexpression association" -> "has evidence" [color=blue, label="has evidence", - lp="1822.9,221.5", - pos="e,1673.8,194.19 2044.2,261.18 1961.6,257 1863.3,247.96 1776.4,229 1744.3,221.98 1709.4,209.06 1683.1,198.12", + lp="1855.9,221.5", + pos="e,1679,193.55 2849.9,264.59 2556.4,264.49 2003.9,259.99 1809.4,229 1767.8,222.36 1722,208.37 1688.6,196.87", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -116,8 +116,8 @@ digraph { width=3.015]; "gene to gene coexpression association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1958.9,221.5", - pos="e,1855,195.94 2061.5,256.54 1993.8,251.44 1924.5,242.98 1894.4,229 1882,223.23 1870.7,213.26 1861.8,203.74", + lp="2011.9,221.5", + pos="e,1869.4,195.64 2852,262.18 2563.4,258.73 2032.5,249.66 1947.4,229 1923.2,223.12 1897.9,211.28 1878.3,200.6", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -126,8 +126,8 @@ digraph { width=3.015]; "gene to gene coexpression association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2125.4,221.5", - pos="e,2046.3,195.46 2091.1,252.67 2063.3,247.5 2039.6,239.97 2030.4,229 2022.7,219.76 2028.4,210.01 2038.2,201.6", + lp="2184.4,221.5", + pos="e,2076.7,196.1 2851.2,262.85 2583,260.38 2118.4,252.69 2089.4,229 2082.7,223.45 2079.3,214.81 2077.8,206.27", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -136,8 +136,8 @@ digraph { width=3.015]; "gene to gene coexpression association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2335.9,221.5", - pos="e,2254.4,193.23 2224.4,246.85 2222.9,236.48 2223,223.49 2229.4,214 2233.7,207.77 2239.2,202.65 2245.5,198.43", + lp="2393.9,221.5", + pos="e,2294.7,195.83 2852.8,261.69 2636.8,258.06 2306.7,249.23 2287.4,229 2280.6,221.87 2283.2,212.53 2288.7,203.85", style=solid]; timepoint [color=blue, height=0.5, @@ -146,8 +146,8 @@ digraph { width=1.5346]; "gene to gene coexpression association" -> timepoint [color=blue, label=timepoint, - lp="2498.4,221.5", - pos="e,2481.7,195.66 2370.4,253.15 2395.2,247.83 2420.2,240.12 2442.4,229 2454.7,222.87 2466,212.85 2474.9,203.39", + lp="2550.4,221.5", + pos="e,2497,196.26 2854.5,261.07 2715.1,257.29 2543,248.66 2515.4,229 2507.8,223.52 2502.9,214.66 2499.8,205.91", style=solid]; "original subject" [color=blue, height=0.5, @@ -156,8 +156,8 @@ digraph { width=1.0652]; "gene to gene coexpression association" -> "original subject" [color=blue, label="original subject", - lp="2613.4,221.5", - pos="e,2586.3,193.57 2360.1,252.04 2435.6,244.65 2518.7,235.38 2535.4,229 2537.9,228.05 2559.3,212.91 2578,199.53", + lp="2649.4,221.5", + pos="e,2595.3,195.28 2854.1,261.08 2739.9,257.3 2611.6,248.67 2593.4,229 2587.3,222.33 2588,213.1 2591.2,204.39", style=solid]; "original predicate" [color=blue, height=0.5, @@ -166,9 +166,8 @@ digraph { width=1.5887]; "gene to gene coexpression association" -> "original predicate" [color=blue, label="original predicate", - lp="2754.9,221.5", - pos="e,2708.6,196.09 2362.1,252.31 2383.6,250.49 2405.6,248.66 2426.4,247 2480.6,242.67 2621,251.64 2670.4,229 2682.6,223.41 2693.5,213.47 \ -2702,203.92", + lp="2777.9,221.5", + pos="e,2712.5,195.83 2875.4,255.89 2800.7,250.46 2726,241.89 2714.4,229 2708.8,222.71 2708.3,214.04 2709.8,205.68", style=solid]; "original object" [color=blue, height=0.5, @@ -177,135 +176,251 @@ digraph { width=1.0652]; "gene to gene coexpression association" -> "original object" [color=blue, label="original object", - lp="2882.9,221.5", - pos="e,2834.5,196.14 2359.4,252.01 2381.7,250.18 2404.7,248.43 2426.4,247 2448.3,245.56 2803.3,242.64 2820.4,229 2827.4,223.44 2831.1,\ -214.68 2833,206.04", + lp="2908.9,221.5", + pos="e,2838.1,196.37 2925.5,250.59 2895.9,245.24 2869.1,238.14 2857.4,229 2850.1,223.23 2845,214.58 2841.5,206.09", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2967.4,178", + width=2.1304]; + "gene to gene coexpression association" -> "subject category" [color=blue, + label="subject category", + lp="3027.9,221.5", + pos="e,2963.6,196.01 2988.3,247.52 2980.4,242.76 2973.3,236.7 2968.4,229 2964.2,222.26 2962.8,213.93 2962.9,206.01", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3138.4,178", + width=2.1304]; + "gene to gene coexpression association" -> "object category" [color=blue, + label="object category", + lp="3159.9,221.5", + pos="e,3122.5,195.89 3063.7,247.1 3071.5,241.57 3080,235.25 3087.4,229 3097,220.99 3106.9,211.56 3115.4,203.06", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3271.4,178", + width=1.0652]; + "gene to gene coexpression association" -> "subject closure" [color=blue, + label="subject closure", + lp="3294.9,221.5", + pos="e,3259.1,195.04 3158.1,250.96 3179.3,245.87 3200.5,238.8 3219.4,229 3231.9,222.54 3243.4,212.16 3252.4,202.52", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3370.4,178", + width=1.0652]; + "gene to gene coexpression association" -> "object closure" [color=blue, + label="object closure", + lp="3414.4,221.5", + pos="e,3369.2,196.03 3172.8,252.34 3255.1,244.65 3346,234.95 3353.4,229 3360.5,223.3 3364.7,214.52 3367.1,205.89", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3503.4,178", + width=2.1304]; + "gene to gene coexpression association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3571.9,221.5", + pos="e,3496.3,195.96 3172.6,252.33 3194,250.52 3215.8,248.69 3236.4,247 3288,242.79 3423.5,254.64 3468.4,229 3478.1,223.48 3485.7,214.08 \ +3491.4,204.91", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3696.4,178", + width=2.1304]; + "gene to gene coexpression association" -> "object category closure" [color=blue, + label="object category closure", + lp="3762.9,221.5", + pos="e,3690.1,196.08 3168.8,251.99 3191.4,250.15 3214.6,248.4 3236.4,247 3283.8,243.97 3622.1,252.38 3663.4,229 3672.9,223.62 3680.2,\ +214.25 3685.5,205.05", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3886.4,178", + width=1.0652]; + "gene to gene coexpression association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3935.4,221.5", + pos="e,3879.1,196.17 3167.5,251.86 3190.4,250.01 3214.1,248.28 3236.4,247 3270.5,245.04 3820.3,245 3850.4,229 3860.5,223.68 3868.4,214.18 \ +3874.2,204.88", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4045.4,178", + width=1.0652]; + "gene to gene coexpression association" -> "object namespace" [color=blue, + label="object namespace", + lp="4088.4,221.5", + pos="e,4037.7,195.73 3167,251.79 3190.1,249.93 3214,248.23 3236.4,247 3279.2,244.67 3969.3,248.49 4007.4,229 4017.9,223.66 4026.3,213.98 \ +4032.5,204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4196.4,178", + width=1.0652]; + "gene to gene coexpression association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4248.4,221.5", + pos="e,4188.1,195.76 3166.4,251.76 3189.7,249.89 3213.8,248.19 3236.4,247 3287.5,244.31 4110.6,251.59 4156.4,229 4167.3,223.66 4176.1,\ +213.84 4182.7,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4367.4,178", + width=1.0652]; + "gene to gene coexpression association" -> "object label closure" [color=blue, + label="object label closure", + lp="4413.9,221.5", + pos="e,4358.8,195.79 3166.2,251.73 3189.5,249.86 3213.7,248.16 3236.4,247 3296.9,243.91 4271.9,255.36 4326.4,229 4337.4,223.69 4346.5,\ +213.87 4353.3,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4508.4,178", + width=2.347]; + "gene to gene coexpression association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4569.9,221.5", + pos="e,4506,196.44 3165.9,251.71 3189.3,249.83 3213.6,248.14 3236.4,247 3271.1,245.26 4458.6,248.44 4487.4,229 4495.3,223.72 4500.2,214.9 \ +4503.3,206.13", style=solid]; type [height=0.5, - pos="2922.4,178", + pos="4642.4,178", width=0.86659]; "gene to gene coexpression association" -> type [color=blue, label=type, - lp="2959.4,221.5", - pos="e,2934.8,194.84 2358,251.93 2380.8,250.08 2404.3,248.34 2426.4,247 2454.8,245.28 2918.7,249.48 2938.4,229 2945,222.19 2943.6,212.67 \ -2939.6,203.76", + lp="4666.4,221.5", + pos="e,4648.4,196.12 3165.6,251.7 3189.2,249.82 3213.5,248.13 3236.4,247 3256,246.04 4629.7,242.91 4643.4,229 4649.3,223.03 4650.6,214.43 \ +4650,206.05", style=solid]; category [height=0.5, - pos="3023.4,178", + pos="4743.4,178", width=1.4263]; "gene to gene coexpression association" -> category [color=blue, label=category, - lp="3029.9,221.5", - pos="e,3013.9,195.75 2357.8,251.9 2380.6,250.05 2404.2,248.31 2426.4,247 2487.8,243.37 2923.8,255.23 2979.4,229 2990.9,223.58 3000.7,\ -213.61 3008,203.99", + lp="4742.9,221.5", + pos="e,4730.4,195.44 3165.6,251.69 3189.2,249.81 3213.5,248.12 3236.4,247 3276.7,245.03 4648.8,243.42 4686.4,229 4700.5,223.59 4713.5,\ +212.98 4723.4,202.93", style=solid]; subject [height=0.5, - pos="3137.4,178", + pos="4857.4,178", width=1.2277]; "gene to gene coexpression association" -> subject [color=blue, label=subject, - lp="3121.4,221.5", - pos="e,3120.7,194.92 2357.5,251.84 2380.4,249.99 2404.1,248.27 2426.4,247 2497.4,242.96 2998,251.18 3065.4,229 3082.8,223.31 3099.6,212 \ -3112.7,201.57", + lp="4837.4,221.5", + pos="e,4839.4,194.55 3165.6,251.68 3189.2,249.8 3213.5,248.12 3236.4,247 3322,242.83 4696.3,253.33 4778.4,229 4797.7,223.3 4816.8,211.43 \ +4831.4,200.69", style=solid]; object [height=0.5, - pos="3180.4,91", + pos="4900.4,91", width=1.0832]; "gene to gene coexpression association" -> object [color=blue, label=object, - lp="3223.4,178", - pos="e,3193.8,108.09 2357,251.82 2380.1,249.96 2404,248.24 2426.4,247 2466.7,244.78 3113.8,243.33 3151.4,229 3193.5,212.98 3198.1,186.73 \ -3203.4,142 3204.2,135.38 3205.3,133.39 3203.4,127 3202.4,123.55 3200.9,120.13 3199.2,116.85", + lp="4944.4,178", + pos="e,4913.8,108.09 3165.4,251.69 3189,249.8 3213.4,248.11 3236.4,247 3281.7,244.81 4824.6,243.8 4867.4,229 4890.2,221.13 4897.3,216.2 \ +4910.4,196 4923.9,175.3 4920.5,166.51 4923.4,142 4924.2,135.38 4925.3,133.39 4923.4,127 4922.4,123.55 4920.9,120.13 4919.2,116.85", style=solid]; predicate [height=0.5, - pos="3334.4,178", + pos="5054.4,178", width=1.5165]; "gene to gene coexpression association" -> predicate [color=blue, label=predicate, - lp="3307.4,221.5", - pos="e,3310.6,194.26 2356.7,251.8 2379.9,249.93 2403.9,248.22 2426.4,247 2515.8,242.17 3144.5,250.02 3231.4,229 3256.3,222.99 3282.2,\ -210.4 3301.8,199.35", + lp="5027.4,221.5", + pos="e,5030.6,194.35 3165.4,251.68 3189,249.79 3213.4,248.11 3236.4,247 3331.6,242.42 4858.7,250.83 4951.4,229 4976.3,223.14 5002.2,210.55 \ +5021.8,199.46", style=solid]; "quantifier qualifier" [height=0.5, - pos="3504.4,178", + pos="5224.4,178", width=2.7081]; "gene to gene coexpression association" -> "quantifier qualifier" [color=blue, label="quantifier qualifier", - lp="3475.4,221.5", - pos="e,3465.7,194.62 2356.4,251.76 2379.7,249.89 2403.8,248.19 2426.4,247 2630.4,236.26 3143.9,261.97 3345.4,229 3383.4,222.78 3424.9,\ -209.52 3456,198.21", + lp="5195.4,221.5", + pos="e,5186,194.61 3165.4,251.67 3189,249.78 3213.4,248.1 3236.4,247 3439.4,237.3 4864.7,260.83 5065.4,229 5103.6,222.95 5145.2,209.6 \ +5176.3,198.22", style=solid]; "expression site" [color=blue, height=0.5, label="anatomical entity", - pos="3711.4,178", + pos="5431.4,178", width=2.5456]; "gene to gene coexpression association" -> "expression site" [color=blue, label="expression site", - lp="3665.9,221.5", - pos="e,3672.2,194.29 2356.2,251.72 2379.5,249.85 2403.7,248.16 2426.4,247 2550.7,240.67 3423.5,248.23 3546.4,229 3586.4,222.75 3630.1,\ -209.19 3662.5,197.76", + lp="5385.9,221.5", + pos="e,5392.2,194.37 3165.1,251.67 3188.8,249.78 3213.3,248.09 3236.4,247 3349.1,241.67 5154.9,246.03 5266.4,229 5306.4,222.9 5350.1,\ +209.32 5382.5,197.85", style=solid]; "stage qualifier" [color=blue, height=0.5, label="life stage", - pos="3875.4,178", + pos="5595.4,178", width=1.4985]; "gene to gene coexpression association" -> "stage qualifier" [color=blue, label="stage qualifier", - lp="3835.9,221.5", - pos="e,3843.8,192.65 2355.9,251.7 2379.3,249.82 2403.6,248.14 2426.4,247 2570.5,239.83 3582.2,252.95 3724.4,229 3762.6,222.57 3804.2,\ -208.2 3834.1,196.5", + lp="5555.9,221.5", + pos="e,5563.8,192.71 3165.1,251.66 3188.8,249.76 3213.3,248.08 3236.4,247 3359,241.25 5323.4,249.02 5444.4,229 5482.6,222.68 5524.3,208.3 \ +5554.1,196.57", style=solid]; "phenotypic state" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="4096.4,178", + pos="5816.4,178", width=4.1344]; "gene to gene coexpression association" -> "phenotypic state" [color=blue, label="phenotypic state", - lp="4030.4,221.5", - pos="e,4045.2,194.92 2355.6,251.69 2379.2,249.81 2403.5,248.12 2426.4,247 2589,239.03 3729.9,249.42 3891.4,229 3940.6,222.78 3995.1,209.16 \ -4035.5,197.71", + lp="5750.4,221.5", + pos="e,5765.2,194.99 3165.1,251.65 3188.8,249.75 3213.3,248.08 3236.4,247 3500,234.7 5349.5,261.48 5611.4,229 5660.6,222.9 5715.1,209.27 \ +5755.5,197.78", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2473.4,265", + pos="3283.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2604.4,265", + pos="3414.4,265", width=2.0762]; subject -> object [label=relation, - lp="3175.4,134.5", - pos="e,3162.5,107.23 3138.5,159.55 3139.7,149.57 3142.2,137.07 3147.4,127 3149.7,122.68 3152.6,118.52 3155.8,114.66"]; + lp="4895.4,134.5", + pos="e,4882.5,107.23 4858.5,159.55 4859.7,149.57 4862.2,137.07 4867.4,127 4869.7,122.68 4872.6,118.52 4875.8,114.66"]; relation [height=0.5, - pos="3125.4,18", + pos="4845.4,18", width=1.2999]; - subject -> relation [pos="e,3126.7,36.188 3136.1,159.79 3134.1,132.48 3130,78.994 3127.5,46.38", + subject -> relation [pos="e,4846.7,36.188 4856.1,159.79 4854.1,132.48 4850,78.994 4847.5,46.38", style=dotted]; "gene to gene association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2807.4,265", + pos="3617.4,265", width=3.0692]; - object -> relation [pos="e,3138.3,35.54 3168,73.889 3161,64.939 3152.3,53.617 3144.5,43.584", + object -> relation [pos="e,4858.3,35.54 4888,73.889 4881,64.939 4872.3,53.617 4864.5,43.584", style=dotted]; "gene to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3046.4,265", + pos="3856.4,265", width=3.0692]; "gene to gene coexpression association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3252.4,265", + pos="4062.4,265", width=2.1665]; "gene expression mixin_quantifier qualifier" [color=blue, height=0.5, label="ontology class", - pos="3425.4,265", + pos="4235.4,265", width=2.1304]; } diff --git a/graphviz/gene_to_gene_coexpression_association.svg b/graphviz/gene_to_gene_coexpression_association.svg index 24be0e5afd..521216a62e 100644 --- a/graphviz/gene_to_gene_coexpression_association.svg +++ b/graphviz/gene_to_gene_coexpression_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene coexpression association - -gene to gene coexpression association + +gene to gene coexpression association @@ -24,8 +24,8 @@ gene to gene coexpression association->gene to gene association - - + + is_a @@ -37,8 +37,8 @@ gene to gene coexpression association->gene expression mixin - - + + uses @@ -50,9 +50,9 @@ gene to gene coexpression association->id - + -id +id @@ -63,9 +63,9 @@ gene to gene coexpression association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ gene to gene coexpression association->name - - -name + + +name @@ -89,9 +89,9 @@ gene to gene coexpression association->description - - -description + + +description @@ -102,9 +102,9 @@ gene to gene coexpression association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ gene to gene coexpression association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ gene to gene coexpression association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ gene to gene coexpression association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ gene to gene coexpression association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ gene to gene coexpression association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ gene to gene coexpression association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ gene to gene coexpression association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ gene to gene coexpression association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ gene to gene coexpression association->original subject - - -original subject + + +original subject @@ -232,9 +232,9 @@ gene to gene coexpression association->original predicate - - -original predicate + + +original predicate @@ -245,187 +245,330 @@ gene to gene coexpression association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to gene coexpression association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to gene coexpression association->object category + + +object category + + + +subject closure + +string + + + +gene to gene coexpression association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to gene coexpression association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to gene coexpression association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to gene coexpression association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to gene coexpression association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to gene coexpression association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to gene coexpression association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to gene coexpression association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to gene coexpression association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to gene coexpression association->type - - -type + + +type - + category - -category + +category - + gene to gene coexpression association->category - - -category + + +category - + subject - -subject + +subject - + gene to gene coexpression association->subject - - -subject + + +subject - + object - -object + +object - + gene to gene coexpression association->object - - -object + + +object - + predicate - -predicate + +predicate - + gene to gene coexpression association->predicate - - -predicate + + +predicate - + quantifier qualifier - -quantifier qualifier + +quantifier qualifier - + gene to gene coexpression association->quantifier qualifier - - -quantifier qualifier + + +quantifier qualifier - + expression site - -anatomical entity + +anatomical entity - + gene to gene coexpression association->expression site - - -expression site + + +expression site - + stage qualifier - -life stage + +life stage - + gene to gene coexpression association->stage qualifier - - -stage qualifier + + +stage qualifier - + phenotypic state - -disease or phenotypic feature + +disease or phenotypic feature - + gene to gene coexpression association->phenotypic state - - -phenotypic state + + +phenotypic state - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to gene association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene to gene association_object - -gene or gene product + +gene or gene product - + gene to gene coexpression association_predicate - -predicate type + +predicate type - + gene expression mixin_quantifier qualifier - -ontology class + +ontology class diff --git a/graphviz/gene_to_gene_family_association.gv b/graphviz/gene_to_gene_family_association.gv index 59ae0aa678..03144018d8 100644 --- a/graphviz/gene_to_gene_family_association.gv +++ b/graphviz/gene_to_gene_family_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3016,283"]; + graph [bb="0,0,4748,283"]; node [label="\N"]; "gene to gene family association" [height=0.5, label="gene to gene family association", - pos="1551.4,265", + pos="2468.4,265", width=4.3691]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to gene family association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1394.4,263.85 1101.3,262.88 481.32,257.42 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2311.3,263.54 1841.5,261.88 467.08,254.85 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to gene family association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1395.4,262.54 1125.6,259.47 582.6,250.74 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2311.8,263.05 1860.6,260.07 578.1,249.86 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene family association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1396.6,261.67 1149.8,257.48 678.06,247.32 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2312.2,262.82 1878.3,259.33 678.89,248.07 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene family association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1395.8,262.05 1167.2,258.54 751.65,249.51 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2311.8,263.15 1892.3,260.59 763.69,251.65 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene family association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1395.2,262.8 1187.1,260.29 829.96,252.59 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2311.3,263.69 1907.3,262.51 852.6,256.76 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene family association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1396.5,261.67 1219.3,258.08 940.43,249.34 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2311.6,263.52 1930.7,261.94 977.64,255.38 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene to gene family association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1397.4,261.3 1287.3,257.63 1136.1,249.04 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2311.1,264.31 1987.5,264.29 1257,260.6 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to gene family association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1403.1,258.9 1321.6,254.3 1218.8,245.56 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2311.1,264.36 2010.8,264.29 1365.8,260.34 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to gene family association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1418.7,255.33 1365.6,250.12 1304.1,241.9 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2311.1,264.32 2035.4,264.05 1475.7,259.59 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "gene to gene family association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1462.8,250.03 1435.4,244.66 1405.4,237.69 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2311.5,263.61 2065,262.17 1598.3,255.85 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "gene to gene family association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1506.6,247.63 1497.9,242.75 1489.6,236.61 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2313.9,261.45 2076.2,257.01 1641.1,246.6 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "gene to gene family association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.4,247.25 1591.3,241.57 1602.4,235.12 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2313.4,261.78 2098.7,257.99 1734.4,248.68 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "gene to gene family association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1662.5,252.19 1731.5,244.44 1809.9,234.71 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,\ -202.83 1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2318.1,259.63 2157.3,254.2 1923.3,243.81 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "gene to gene family association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.19 1660.9,252.08 1680.1,250.21 1699.8,248.43 1718.4,247 1794.5,241.13 1990.3,256.86 2061.4,229 2069.3,225.89 2084,213.75 \ -2096.8,202.21", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2329.3,256.52 2245.3,250.77 2151.6,241.65 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "gene to gene family association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1660.5,251.94 1679.7,250.08 1699.6,248.34 1718.4,247 1815.1,240.09 2062,258.54 2154.4,229 2166,225.28 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2318.1,259.68 2271.8,254.97 2229.2,245.95 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "gene to gene family association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.5 1659.6,251.88 1679.1,250 1699.3,248.27 1718.4,247 1781.7,242.78 2230.2,252.04 2289.4,229 2297.1,225.98 2311.2,213.98 \ -2323.5,202.5", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2381.5,249.91 2359.9,244.58 2341.1,237.66 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,207 @@ digraph { width=1.0652]; "gene to gene family association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.43 1659.1,251.81 1678.8,249.93 1699.2,248.21 1718.4,247 1758.4,244.47 2406.1,251.31 2439.4,229 2447.3,223.7 2452.4,\ -214.89 2455.6,206.12", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "gene to gene family association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2539.6,248.91 2551.5,244.01 2563,237.55 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "gene to gene family association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2585.2,252.88 2634,246.99 2684.5,238.91 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "gene to gene family association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.55 2580.7,252.32 2598.9,250.49 2617.7,248.66 2635.4,247 2682,242.63 2802.6,248.14 2845.4,229 2858.3,223.21 2870.1,212.91 \ +2879.2,203.16", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "gene to gene family association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2997,196.24 2577.9,252.07 2597.1,250.21 2616.8,248.43 2635.4,247 2673.7,244.06 2949.6,251.88 2980.4,229 2987.7,223.54 2992.1,214.81 \ +2994.7,206.16", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "gene to gene family association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.12 2577,251.95 2596.4,250.08 2616.5,248.33 2635.4,247 2686.5,243.4 3051.4,253.56 3096.4,229 3106.2,223.67 3113.8,214.3 \ +3119.4,205.1", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "gene to gene family association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.11 2576.1,251.85 2595.8,249.97 2616.2,248.24 2635.4,247 2671.8,244.65 3260.7,247.19 3292.4,229 3301.6,223.71 3308.4,\ +214.48 3313.3,205.38", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "gene to gene family association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.19 2575.6,251.8 2595.5,249.91 2616.1,248.19 2635.4,247 2682.2,244.13 3437.1,251.08 3478.4,229 3488.2,223.76 3495.9,\ +214.4 3501.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "gene to gene family association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.74 2575.6,251.75 2595.5,249.86 2616,248.16 2635.4,247 2690.9,243.68 3586,254.45 3635.4,229 3645.7,223.68 3653.9,213.99 \ +3659.9,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "gene to gene family association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.77 2575.2,251.75 2595.2,249.85 2615.9,248.14 2635.4,247 2667.3,245.13 3755.8,243.23 3784.4,229 3795.1,223.66 3803.8,\ +213.84 3810.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "gene to gene family association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2575.2,251.72 2595.2,249.82 2615.9,248.12 2635.4,247 2672,244.89 3921.5,245.1 3954.4,229 3965.3,223.69 3974.1,213.87 \ +3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "gene to gene family association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2575.2,251.7 2595.2,249.8 2615.9,248.11 2635.4,247 2676.4,244.67 4079.4,248.96 4115.4,229 4124.9,223.75 4131.9,214.39 \ +4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "gene to gene family association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.3,195.51 1658.6,251.8 1678.5,249.91 1699.1,248.19 1718.4,247 1741.7,245.57 2543,245.7 2559.4,229 2565.6,222.66 2565.4,213.61 \ -2562.9,204.96", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2574.7,251.72 2594.9,249.81 2615.8,248.11 2635.4,247 2658.1,245.72 4257.3,244.03 4274.4,229 4280.9,223.32 4283.4,\ +214.65 4284.1,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "gene to gene family association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.84 1658.6,251.78 1678.5,249.89 1699.1,248.18 1718.4,247 1767.4,244.01 2556.4,248.47 2601.4,229 2613.8,223.65 2624.6,\ -213.55 2632.9,203.82", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2574.7,251.72 2594.9,249.81 2615.8,248.1 2635.4,247 2682.1,244.38 4275.3,244.63 4319.4,229 4334.6,223.59 4349,212.84 \ +4360.1,202.68", style=solid]; subject [height=0.5, - pos="2764.4,178", + pos="4496.4,178", width=1.2277]; "gene to gene family association" -> subject [color=blue, label=subject, - lp="2747.4,221.5", - pos="e,2747.4,194.74 1658.6,251.76 1678.5,249.87 1699,248.16 1718.4,247 1772.3,243.76 2638.9,245.29 2690.4,229 2708.4,223.31 2726,211.72 \ -2739.5,201.14", + lp="4473.4,221.5", + pos="e,4477.7,194.32 2574.7,251.71 2594.9,249.8 2615.8,248.1 2635.4,247 2734,241.49 4318.4,255.93 4413.4,229 4433.6,223.29 4453.7,211.3 \ +4469.2,200.49", style=solid]; object [height=0.5, - pos="2807.4,91", + pos="4539.4,91", width=1.0832]; "gene to gene family association" -> object [color=blue, label=object, - lp="2850.4,178", - pos="e,2820.8,108.09 1658.2,251.77 1678.2,249.87 1698.9,248.16 1718.4,247 1777.1,243.52 2722.2,249.36 2777.4,229 2819.9,213.33 2825.1,\ -186.96 2830.4,142 2831.2,135.38 2832.3,133.39 2830.4,127 2829.4,123.55 2827.9,120.13 2826.1,116.85", + lp="4583.4,178", + pos="e,4552.8,108.09 2574.7,251.7 2594.9,249.79 2615.8,248.09 2635.4,247 2687.2,244.12 4454.1,245.12 4503.4,229 4527.3,221.18 4535.3,\ +216.87 4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,\ +116.85", style=solid]; predicate [height=0.5, - pos="2961.4,178", + pos="4693.4,178", width=1.5165]; "gene to gene family association" -> predicate [color=blue, label=predicate, - lp="2934.4,221.5", - pos="e,2937.6,194.31 1658.2,251.75 1678.2,249.85 1698.9,248.14 1718.4,247 1844.9,239.58 2735.2,258.36 2858.4,229 2883.3,223.07 2909.1,\ -210.48 2928.7,199.42", + lp="4666.4,221.5", + pos="e,4669.6,194.36 2574.7,251.69 2594.9,249.78 2615.8,248.09 2635.4,247 2743.8,240.99 4484.7,253.82 4590.4,229 4615.3,223.16 4641.2,\ +210.56 4660.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1765.4,265", + pos="2682.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1896.4,265", + pos="2813.4,265", width=2.0762]; subject -> object [label=relation, - lp="2802.4,134.5", - pos="e,2789.5,107.23 2765.5,159.55 2766.7,149.57 2769.2,137.07 2774.4,127 2776.6,122.68 2779.5,118.52 2782.7,114.66"]; + lp="4534.4,134.5", + pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; relation [height=0.5, - pos="2752.4,18", + pos="4484.4,18", width=1.2999]; - subject -> relation [pos="e,2753.7,36.188 2763.1,159.79 2761,132.48 2757,78.994 2754.5,46.38", + subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", style=dotted]; "gene to gene family association_subject" [color=blue, height=0.5, label=gene, - pos="2022.4,265", + pos="2939.4,265", width=0.92075]; - object -> relation [pos="e,2765.2,35.54 2794.9,73.889 2788,64.939 2779.2,53.617 2771.4,43.584", + object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", style=dotted]; "gene to gene family association_object" [color=blue, height=0.5, label="gene family", - pos="2138.4,265", + pos="3055.4,265", width=1.8054]; "gene to gene family association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2299.4,265", + pos="3216.4,265", width=2.1665]; } diff --git a/graphviz/gene_to_gene_family_association.svg b/graphviz/gene_to_gene_family_association.svg index 46112ba0f2..b00349156d 100644 --- a/graphviz/gene_to_gene_family_association.svg +++ b/graphviz/gene_to_gene_family_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene family association - -gene to gene family association + +gene to gene family association @@ -24,9 +24,9 @@ gene to gene family association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to gene family association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to gene family association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene family association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene family association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene family association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene family association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene to gene family association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to gene family association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ gene to gene family association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ gene to gene family association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ gene to gene family association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ gene to gene family association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ gene to gene family association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ gene to gene family association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ gene to gene family association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ gene to gene family association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to gene family association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to gene family association->object category + + +object category + + + +subject closure + +string + + + +gene to gene family association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to gene family association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to gene family association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to gene family association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to gene family association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to gene family association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to gene family association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to gene family association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to gene family association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to gene family association->type - - -type + + +type - + category - -category + +category - + gene to gene family association->category - - -category + + +category - + subject - -subject + +subject - + gene to gene family association->subject - - -subject + + +subject - + object - -object + +object - + gene to gene family association->object - - -object + + +object - + predicate - -predicate + +predicate - + gene to gene family association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to gene family association_subject - -gene + +gene - + object->relation - - + + - + gene to gene family association_object - -gene family + +gene family - + gene to gene family association_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_gene_homology_association.gv b/graphviz/gene_to_gene_homology_association.gv index 8219d47cb2..3aab775d34 100644 --- a/graphviz/gene_to_gene_homology_association.gv +++ b/graphviz/gene_to_gene_homology_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3121.4,283"]; + graph [bb="0,0,4853.4,283"]; node [label="\N"]; "gene to gene homology association" [height=0.5, label="gene to gene homology association", - pos="1677.4,265", + pos="2594.4,265", width=4.8024]; "gene to gene association" [height=0.5, pos="125.44,178", width=3.4844]; "gene to gene homology association" -> "gene to gene association" [label=is_a, - lp="408.44,221.5", - pos="e,188.35,193.58 1505.8,262.65 1207.3,259.74 604.53,251.25 394.44,229 327.4,221.9 252.02,207.31 198.15,195.71"]; + lp="406.44,221.5", + pos="e,187.32,193.67 2422.6,262.94 1939.5,259.74 591.68,249.09 392.44,229 325.77,222.28 250.85,207.61 197.38,195.89"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to gene homology association" -> id [color=blue, label=id, - lp="526.44,221.5", - pos="e,336.42,190.01 1506.2,262.36 1231.7,259.14 705.15,250.34 519.44,229 445.57,220.51 427.11,215.79 355.44,196 352.33,195.14 349.13,\ -194.18 345.93,193.17", + lp="522.44,221.5", + pos="e,336.43,189.98 2422.7,262.95 1958.6,259.85 702.07,249.63 515.44,229 443.27,221.02 425.38,215.5 355.44,196 352.33,195.13 349.13,\ +194.17 345.93,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene homology association" -> iri [color=blue, label=iri, - lp="645.44,221.5", - pos="e,441.05,190.17 1507.9,261.42 1257.6,257.08 800.85,246.96 637.44,229 558.33,220.3 538.59,215.53 461.44,196 458.01,195.13 454.48,\ -194.16 450.94,193.14", + lp="635.44,221.5", + pos="e,441.35,190.2 2422.7,262.7 1976.5,259.07 802.86,247.84 627.44,229 552.65,220.97 534.26,214.85 461.44,196 458.06,195.13 454.58,194.16 \ +451.1,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene homology association" -> name [color=blue, label=name, - lp="749.44,221.5", - pos="e,566.44,191.25 1507,261.82 1275.7,258.15 874.53,249.07 729.44,229 676.21,221.64 616.65,205.95 576.08,194.1", + lp="742.44,221.5", + pos="e,565.4,191.54 2422.4,263.06 1991.3,260.37 887.73,251.38 722.44,229 671.3,222.08 614.29,206.51 575.18,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene homology association" -> description [color=blue, label=description, - lp="867.94,221.5", - pos="e,712.76,193.92 1506,262.61 1296.1,259.91 952.92,252.02 827.44,229 791.17,222.35 751.67,208.91 722.31,197.64", + lp="862.94,221.5", + pos="e,711.49,194.14 2422,263.65 2007.3,262.36 976.71,256.42 822.44,229 787.38,222.77 749.38,209.4 721.08,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene homology association" -> "has attribute" [color=blue, label="has attribute", - lp="1010.4,221.5", - pos="e,852.79,192.68 1507.8,261.37 1330.2,257.6 1063.7,248.78 963.44,229 928.22,222.05 889.94,208.03 862.16,196.6", + lp="1008.4,221.5", + pos="e,852.02,192.82 2421.9,263.45 2031.2,261.76 1101.8,255.02 961.44,229 926.48,222.52 888.61,208.39 861.24,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene to gene homology association" -> negated [color=blue, label=negated, - lp="1159.4,221.5", - pos="e,973.83,190.35 1509,260.8 1400.5,256.87 1256.5,248.18 1130.4,229 1079.3,221.22 1022,205.22 983.65,193.4", + lp="1164.4,221.5", + pos="e,973.64,190.46 2421.4,264.31 2090.5,264.17 1379.1,260.1 1135.4,229 1082.1,222.2 1022.5,205.66 983.19,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to gene homology association" -> qualifiers [color=blue, label=qualifiers, - lp="1287.9,221.5", - pos="e,1121.4,193.25 1517.3,258.2 1437.7,253.44 1340.5,244.77 1254.4,229 1212.2,221.27 1165.6,207.56 1131.2,196.45", + lp="1304.9,221.5", + pos="e,1122.7,193.07 2421.5,264.35 2114.9,264.15 1488.1,259.81 1271.4,229 1223.6,222.2 1170.6,207.74 1132.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to gene homology association" -> publications [color=blue, label=publications, - lp="1419.4,221.5", - pos="e,1270.2,193.34 1536.4,254.5 1485.3,249.26 1427.3,241.23 1375.4,229 1342.5,221.24 1306.7,208.09 1279.7,197.22", + lp="1452.4,221.5", + pos="e,1274.2,192.71 2421.6,264.3 2140.9,263.88 1598.2,259.03 1408.4,229 1365.3,222.18 1317.8,207.69 1283.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "gene to gene homology association" -> "has evidence" [color=blue, label="has evidence", - lp="1550.9,221.5", - pos="e,1423.3,194.68 1586.7,249.6 1559.9,244.29 1530.7,237.45 1504.4,229 1479.8,221.08 1453.4,209.32 1432.5,199.19", + lp="1606.9,221.5", + pos="e,1431.9,193.61 2422,263.52 2171.9,261.9 1721,255.3 1560.4,229 1519.6,222.3 1474.7,208.48 1441.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "gene to gene homology association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1673.9,221.5", - pos="e,1596.8,196.34 1632.3,247.43 1623.7,242.58 1615.6,236.51 1609.4,229 1604.2,222.52 1600.9,214.16 1598.8,206.15", + lp="1761.9,221.5", + pos="e,1621.5,195.59 2425.2,261.18 2184.7,256.59 1765.7,246.24 1697.4,229 1673.9,223.07 1649.5,211.31 1630.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "gene to gene homology association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1856.4,221.5", - pos="e,1796.7,195.19 1707.4,247.25 1717.4,241.57 1728.4,235.12 1738.4,229 1748.8,222.63 1750.9,220.1 1761.4,214 1769.8,209.16 1778.9,\ -204.28 1787.7,199.76", + lp="1933.4,221.5", + pos="e,1828.2,196.41 2424.5,261.51 2208.2,257.55 1860,248.23 1838.4,229 1832.1,223.34 1829.4,214.82 1828.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "gene to gene homology association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2080.9,221.5", - pos="e,2019.7,194.43 1806.9,253.01 1864.3,247 1924.8,238.79 1951.4,229 1962.9,224.79 1963.6,219.55 1974.4,214 1985.7,208.22 1998.2,202.83 \ -2010.2,198.09", + lp="2141.9,221.5", + pos="e,2044.7,195.97 2430.6,259.17 2270.6,253.62 2049,243.4 2035.4,229 2028.4,221.54 2031.6,212.18 2038.1,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "gene to gene homology association" -> timepoint [color=blue, label=timepoint, - lp="2244.4,221.5", - pos="e,2230.5,195.18 1798.3,252.06 1818.7,250.23 1839.7,248.47 1859.4,247 1932.2,241.6 2119.5,255.72 2187.4,229 2195.4,225.88 2210,213.74 \ -2222.8,202.2", + lp="2297.4,221.5", + pos="e,2248,196.47 2445.2,255.81 2364,250.03 2277.1,241.14 2262.4,229 2255.7,223.41 2251.9,214.91 2249.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "gene to gene homology association" -> "original subject" [color=blue, label="original subject", - lp="2359.4,221.5", - pos="e,2337.3,192.7 1797.3,251.94 1818,250.1 1839.3,248.37 1859.4,247 1952.9,240.64 2191.3,257.59 2280.4,229 2292.1,225.27 2293.2,220.57 \ -2303.4,214 2311.6,208.79 2320.5,203.21 2328.7,198.07", + lp="2396.4,221.5", + pos="e,2345.7,194.92 2433.2,258.48 2391.3,253.49 2354,244.6 2340.4,229 2334.2,221.83 2336,212.39 2340.4,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "gene to gene homology association" -> "original predicate" [color=blue, label="original predicate", - lp="2500.9,221.5", - pos="e,2456.9,195.49 1796.3,251.85 1817.3,250 1839,248.28 1859.4,247 1921.1,243.12 2357.9,251.46 2415.4,229 2423.2,225.98 2437.2,213.98 \ -2449.5,202.49", + lp="2523.9,221.5", + pos="e,2462.4,195.76 2505.8,249.47 2485,244.2 2466.9,237.42 2460.4,229 2455.2,222.16 2455.7,213.39 2458.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "gene to gene homology association" -> "original object" [color=blue, label="original object", - lp="2629.9,221.5", - pos="e,2584.7,196.43 1795.3,251.82 1816.6,249.95 1838.7,248.23 1859.4,247 1898.6,244.67 2532.9,250.86 2565.4,229 2573.3,223.7 2578.4,\ -214.88 2581.7,206.12", + lp="2642.9,221.5", + pos="e,2588.9,196.18 2593,246.8 2592.1,235.16 2590.8,219.55 2589.7,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2720.4,178", + width=2.1304]; + "gene to gene homology association" -> "subject category" [color=blue, + label="subject category", + lp="2768.9,221.5", + pos="e,2716.6,196.4 2666.5,248.57 2678.1,243.72 2689.3,237.35 2698.4,229 2705.2,222.84 2710,214.24 2713.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2891.4,178", + width=2.1304]; + "gene to gene homology association" -> "object category" [color=blue, + label="object category", + lp="2911.9,221.5", + pos="e,2876.6,195.73 2716.7,252.22 2763.8,246.39 2811.3,238.55 2832.4,229 2846.1,222.83 2859,212.54 2869.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3024.4,178", + width=1.0652]; + "gene to gene homology association" -> "subject closure" [color=blue, + label="subject closure", + lp="3047.9,221.5", + pos="e,3012,195.52 2718.3,252.41 2737.7,250.6 2757.6,248.75 2776.4,247 2819.8,242.98 2931.8,246.91 2971.4,229 2984.4,223.17 2996.1,212.86 \ +3005.3,203.12", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3124.4,178", + width=1.0652]; + "gene to gene homology association" -> "object closure" [color=blue, + label="object closure", + lp="3168.4,221.5", + pos="e,3123,196.23 2715.3,252.05 2735.7,250.22 2756.7,248.46 2776.4,247 2813.1,244.29 3077,250.93 3106.4,229 3113.8,223.54 3118.1,214.8 \ +3120.7,206.15", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3257.4,178", + width=2.1304]; + "gene to gene homology association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3326.9,221.5", + pos="e,3250.4,196.11 2713.8,251.94 2734.7,250.09 2756.2,248.35 2776.4,247 2825.9,243.69 3178.9,252.79 3222.4,229 3232.2,223.66 3239.8,\ +214.29 3245.5,205.1", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3449.4,178", + width=2.1304]; + "gene to gene homology association" -> "object category closure" [color=blue, + label="object category closure", + lp="3516.9,221.5", + pos="e,3443.7,196.1 2712.8,251.82 2734,249.96 2755.8,248.25 2776.4,247 2812.1,244.84 3387.5,246.79 3418.4,229 3427.6,223.71 3434.5,214.48 \ +3439.4,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3639.4,178", + width=1.0652]; + "gene to gene homology association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3689.4,221.5", + pos="e,3632.5,196.19 2712.3,251.75 2733.6,249.89 2755.7,248.19 2776.4,247 2822.4,244.36 3563.9,250.69 3604.4,229 3614.3,223.76 3621.9,\ +214.4 3627.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3798.4,178", + width=1.0652]; + "gene to gene homology association" -> "object namespace" [color=blue, + label="object namespace", + lp="3842.4,221.5", + pos="e,3791.1,195.73 2711.8,251.73 2733.3,249.86 2755.5,248.17 2776.4,247 2831.1,243.95 3712.8,254.08 3761.4,229 3771.8,223.68 3780,213.99 \ +3786,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3949.4,178", + width=1.0652]; + "gene to gene homology association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4002.4,221.5", + pos="e,3941.4,195.77 2711.3,251.74 2733,249.85 2755.4,248.15 2776.4,247 2807.9,245.28 3882.2,243.05 3910.4,229 3921.2,223.66 3929.8,213.84 \ +3936.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4120.4,178", + width=1.0652]; + "gene to gene homology association" -> "object label closure" [color=blue, + label="object label closure", + lp="4167.9,221.5", + pos="e,4112.1,195.79 2711.3,251.7 2733,249.82 2755.4,248.13 2776.4,247 2812.6,245.06 4047.9,244.92 4080.4,229 4091.3,223.69 4100.1,213.87 \ +4106.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4273.4,178", + width=2.347]; + "gene to gene homology association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4326.9,221.5", + pos="e,4267.5,196.18 2711.3,251.67 2733,249.79 2755.4,248.11 2776.4,247 2817.1,244.86 4205.9,248.76 4241.4,229 4250.9,223.75 4258,214.39 \ +4263,205.18", style=solid]; type [height=0.5, - pos="2675.4,178", + pos="4407.4,178", width=0.86659]; "gene to gene homology association" -> type [color=blue, label=type, - lp="2707.4,221.5", - pos="e,2685.3,195.51 1795.3,251.75 1816.6,249.89 1838.7,248.19 1859.4,247 1882.4,245.68 2669.4,245.4 2685.4,229 2691.6,222.66 2691.5,\ -213.61 2688.9,204.95", + lp="4425.4,221.5", + pos="e,4410.1,195.98 2711.3,251.65 2733,249.77 2755.4,248.1 2776.4,247 2799,245.83 4383.5,243.9 4400.4,229 4406.9,223.32 4409.4,214.65 \ +4410.1,206.12", style=solid]; category [height=0.5, - pos="2776.4,178", + pos="4508.4,178", width=1.4263]; "gene to gene homology association" -> category [color=blue, label=category, - lp="2780.9,221.5", - pos="e,2765.4,195.84 1794.8,251.78 1816.3,249.9 1838.5,248.19 1859.4,247 1907.6,244.26 2683.2,248.14 2727.4,229 2739.8,223.65 2750.7,\ -213.55 2759,203.81", + lp="4503.9,221.5", + pos="e,4493.7,195.48 2710.8,251.69 2732.6,249.8 2755.2,248.1 2776.4,247 2822.7,244.59 4401.7,244.5 4445.4,229 4460.7,223.59 4475,212.84 \ +4486.2,202.68", style=solid]; subject [height=0.5, - pos="2890.4,178", + pos="4622.4,178", width=1.2277]; "gene to gene homology association" -> subject [color=blue, label=subject, - lp="2873.4,221.5", - pos="e,2873.4,194.73 1794.8,251.74 1816.3,249.87 1838.5,248.17 1859.4,247 1912.5,244.03 2765.7,245.04 2816.4,229 2834.4,223.3 2852,211.72 \ -2865.6,201.13", + lp="4599.4,221.5", + pos="e,4603.7,194.32 2710.8,251.68 2732.6,249.79 2755.2,248.1 2776.4,247 2874.3,241.94 4445.2,255.71 4539.4,229 4559.6,223.29 4579.8,\ +211.3 4595.2,200.49", style=solid]; predicate [height=0.5, - pos="3007.4,178", + pos="4739.4,178", width=1.5165]; "gene to gene homology association" -> predicate [color=blue, label=predicate, - lp="2979.4,221.5", - pos="e,2983.3,194.3 1794.8,251.72 1816.3,249.84 1838.5,248.16 1859.4,247 1975.3,240.6 2790.5,255.75 2903.4,229 2928.5,223.06 2954.6,210.46 \ -2974.4,199.4", + lp="4707.4,221.5", + pos="e,4714.3,194.12 2710.8,251.67 2732.6,249.78 2755.2,248.09 2776.4,247 2879.3,241.71 4528.9,251.28 4629.4,229 4656.2,223.07 4684.3,\ +210.16 4705.4,198.95", style=solid]; object [height=0.5, - pos="2957.4,91", + pos="4689.4,91", width=1.0832]; "gene to gene homology association" -> object [color=blue, label=object, - lp="3099.4,178", - pos="e,2989.5,101.28 1794.3,251.73 1816,249.84 1838.4,248.15 1859.4,247 1923.7,243.51 2955.6,246.91 3017.4,229 3044.5,221.17 3057.7,220.53 \ -3071.4,196 3079.3,182.04 3079.3,173.91 3071.4,160 3056,132.81 3024.9,115.34 2999.1,104.93", + lp="4831.4,178", + pos="e,4719.3,102.76 2710.8,251.66 2732.6,249.77 2755.2,248.09 2776.4,247 2885.7,241.41 4639.8,257.46 4745.4,229 4774.1,221.28 4788.5,\ +221.64 4803.4,196 4826.1,157.11 4770,124.49 4728.7,106.65", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1906.4,265", + pos="2823.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2037.4,265", + pos="2954.4,265", width=2.0762]; subject -> object [label=relation, - lp="2956.4,134.5", - pos="e,2944.8,108.05 2903.4,160.61 2913.3,147.95 2927.3,130.24 2938.5,115.98"]; + lp="4688.4,134.5", + pos="e,4676.8,108.05 4635.4,160.61 4645.3,147.95 4659.3,130.24 4670.5,115.98"]; relation [height=0.5, - pos="2902.4,18", + pos="4634.4,18", width=1.2999]; - subject -> relation [pos="e,2901.1,36.188 2891.7,159.79 2893.8,132.48 2897.9,78.994 2900.4,46.38", + subject -> relation [pos="e,4633.1,36.188 4623.7,159.79 4625.8,132.48 4629.9,78.994 4632.4,46.38", style=dotted]; "gene to gene homology association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2240.4,265", + pos="3157.4,265", width=3.0692]; "gene to gene homology association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2446.4,265", + pos="3363.4,265", width=2.1665]; - object -> relation [pos="e,2915.3,35.54 2945,73.889 2938,64.939 2929.3,53.617 2921.5,43.584", + object -> relation [pos="e,4647.3,35.54 4677,73.889 4670,64.939 4661.3,53.617 4653.5,43.584", style=dotted]; "gene to gene homology association_object" [color=blue, height=0.5, label="gene or gene product", - pos="2652.4,265", + pos="3569.4,265", width=3.0692]; } diff --git a/graphviz/gene_to_gene_homology_association.svg b/graphviz/gene_to_gene_homology_association.svg index 4b8b6dac36..8897657210 100644 --- a/graphviz/gene_to_gene_homology_association.svg +++ b/graphviz/gene_to_gene_homology_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene homology association - -gene to gene homology association + +gene to gene homology association @@ -24,9 +24,9 @@ gene to gene homology association->gene to gene association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to gene homology association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to gene homology association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene homology association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene homology association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene homology association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene homology association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene to gene homology association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to gene homology association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ gene to gene homology association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ gene to gene homology association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ gene to gene homology association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ gene to gene homology association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ gene to gene homology association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ gene to gene homology association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ gene to gene homology association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ gene to gene homology association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to gene homology association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to gene homology association->object category + + +object category + + + +subject closure + +string + + + +gene to gene homology association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to gene homology association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to gene homology association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to gene homology association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to gene homology association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to gene homology association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to gene homology association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to gene homology association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to gene homology association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to gene homology association->type - - -type + + +type - + category - -category + +category - + gene to gene homology association->category - - -category + + +category - + subject - -subject + +subject - + gene to gene homology association->subject - - -subject + + +subject - + predicate - -predicate + +predicate - + gene to gene homology association->predicate - - -predicate + + +predicate - + object - -object + +object - + gene to gene homology association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to gene homology association_subject - -gene or gene product + +gene or gene product - + gene to gene homology association_predicate - -predicate type + +predicate type - + object->relation - - + + - + gene to gene homology association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/gene_to_gene_product_relationship.gv b/graphviz/gene_to_gene_product_relationship.gv index b383e9b15d..f51da91455 100644 --- a/graphviz/gene_to_gene_product_relationship.gv +++ b/graphviz/gene_to_gene_product_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3190.1,283"]; + graph [bb="0,0,4922.1,283"]; node [label="\N"]; "gene to gene product relationship" [height=0.5, label="gene to gene product relationship", - pos="1725.5,265", + pos="2642.5,265", width=4.676]; "sequence feature relationship" [height=0.5, pos="149.49,178", width=4.1524]; "gene to gene product relationship" -> "sequence feature relationship" [label=is_a, - lp="456.49,221.5", - pos="e,219.86,193.89 1558.9,262.39 1262.2,259.04 653.91,249.82 442.49,229 370.03,221.87 288.44,207.41 229.8,195.87"]; + lp="454.49,221.5", + pos="e,218.76,194 2475,262.83 1995.7,259.27 640.47,247.66 440.49,229 368.23,222.26 286.91,207.68 228.64,196"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to gene product relationship" -> id [color=blue, label=id, - lp="574.49,221.5", - pos="e,384.47,190.01 1558.6,262.41 1285.4,259.24 754.19,250.45 567.49,229 493.62,220.51 475.15,215.79 403.49,196 400.38,195.14 397.18,\ -194.18 393.98,193.17", + lp="570.49,221.5", + pos="e,384.47,189.98 2474.9,262.98 2014.2,259.91 750.68,249.7 563.49,229 491.32,221.02 473.43,215.5 403.49,196 400.38,195.13 397.18,194.17 \ +393.98,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene product relationship" -> iri [color=blue, label=iri, - lp="693.49,221.5", - pos="e,489.1,190.17 1560.4,261.5 1311,257.19 849.85,247.07 685.49,229 606.38,220.3 586.64,215.53 509.49,196 506.06,195.13 502.52,194.16 \ -498.99,193.14", + lp="683.49,221.5", + pos="e,489.4,190.2 2475.2,262.74 2032.4,259.14 851.49,247.91 675.49,229 600.7,220.97 582.31,214.85 509.49,196 506.11,195.13 502.63,194.16 \ +499.15,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene product relationship" -> name [color=blue, label=name, - lp="797.49,221.5", - pos="e,614.49,191.25 1559.4,261.89 1328.8,258.26 923.5,249.2 777.49,229 724.26,221.64 664.69,205.95 624.12,194.1", + lp="790.49,221.5", + pos="e,613.44,191.54 2474.7,263.08 2046.8,260.43 936.33,251.45 770.49,229 719.35,222.08 662.34,206.51 623.23,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene product relationship" -> description [color=blue, label=description, - lp="915.99,221.5", - pos="e,760.81,193.92 1558.2,262.66 1348.6,260.01 1001.8,252.17 875.49,229 839.22,222.35 799.72,208.91 770.36,197.64", + lp="910.99,221.5", + pos="e,759.54,194.14 2474.3,263.66 2062.3,262.4 1025.3,256.51 870.49,229 835.43,222.77 797.43,209.4 769.13,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene product relationship" -> "has attribute" [color=blue, label="has attribute", - lp="1058.5,221.5", - pos="e,900.84,192.68 1560.3,261.46 1382.8,257.74 1112.5,248.95 1011.5,229 976.27,222.05 937.98,208.03 910.2,196.6", + lp="1056.5,221.5", + pos="e,900.07,192.82 2474.7,263.47 2086.8,261.82 1150.4,255.13 1009.5,229 974.52,222.52 936.66,208.39 909.29,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene to gene product relationship" -> negated [color=blue, label=negated, - lp="1207.5,221.5", - pos="e,1021.9,190.35 1561.3,260.95 1452.3,257.09 1306.2,248.43 1178.5,229 1127.3,221.22 1070.1,205.22 1031.7,193.4", + lp="1212.5,221.5", + pos="e,1021.7,190.46 2474.2,264.31 2145.4,264.2 1428.3,260.25 1183.5,229 1130.2,222.2 1070.6,205.66 1031.2,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to gene product relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1336,221.5", - pos="e,1169.4,193.25 1568.8,258.41 1488.7,253.69 1389.8,245 1302.5,229 1260.3,221.27 1213.6,207.56 1179.2,196.45", + lp="1353,221.5", + pos="e,1170.8,193.07 2474,264.35 2169.1,264.19 1537.2,259.96 1319.5,229 1271.7,222.2 1218.6,207.74 1180.6,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to gene product relationship" -> publications [color=blue, label=publications, - lp="1467.5,221.5", - pos="e,1318.3,193.34 1586.8,254.73 1535,249.5 1476.1,241.41 1423.5,229 1390.6,221.24 1354.7,208.09 1327.8,197.22", + lp="1500.5,221.5", + pos="e,1322.2,192.71 2474.2,264.31 2194.8,263.93 1647.2,259.19 1456.5,229 1413.4,222.18 1365.9,207.69 1331.9,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "gene to gene product relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1599,221.5", - pos="e,1471.4,194.68 1635.6,249.77 1608.6,244.44 1579,237.54 1552.5,229 1527.9,221.08 1501.5,209.32 1480.6,199.19", + lp="1655,221.5", + pos="e,1480,193.61 2474.4,263.55 2225.3,261.98 1770,255.45 1608.5,229 1567.6,222.3 1522.7,208.48 1489.8,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "gene to gene product relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1722,221.5", - pos="e,1644.9,196.34 1680.7,247.63 1672,242.75 1663.7,236.61 1657.5,229 1652.2,222.52 1648.9,214.16 1646.9,206.15", + lp="1810,221.5", + pos="e,1669.6,195.59 2477.7,261.26 2238,256.71 1814.2,246.35 1745.5,229 1722,223.07 1697.5,211.31 1678.5,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "gene to gene product relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1904.5,221.5", - pos="e,1844.8,195.19 1755.5,247.25 1765.4,241.57 1776.5,235.12 1786.5,229 1796.9,222.63 1798.9,220.1 1809.5,214 1817.9,209.16 1827,204.28 \ -1835.8,199.76", + lp="1981.5,221.5", + pos="e,1876.2,196.41 2477.1,261.59 2261.3,257.69 1908.2,248.37 1886.5,229 1880.1,223.34 1877.5,214.82 1876.6,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "gene to gene product relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2129,221.5", - pos="e,2067.8,194.43 1840.3,251.76 1908.4,244.08 1984.2,234.61 1999.5,229 2010.9,224.79 2011.6,219.55 2022.5,214 2033.8,208.22 2046.3,\ -202.83 2058.3,198.09", + lp="2190,221.5", + pos="e,2092.8,195.97 2482.7,259.3 2322.4,253.79 2097.1,243.52 2083.5,229 2076.5,221.54 2079.7,212.18 2086.1,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "gene to gene product relationship" -> timepoint [color=blue, label=timepoint, - lp="2292.5,221.5", - pos="e,2278.6,195.18 1843.2,252.07 1863.3,250.23 1884,248.46 1903.5,247 1977.2,241.49 2166.7,256.02 2235.5,229 2243.4,225.88 2258.1,213.74 \ -2270.9,202.2", + lp="2345.5,221.5", + pos="e,2296,196.47 2496,256.01 2414,250.23 2325.3,241.28 2310.5,229 2303.7,223.41 2300,214.91 2297.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "gene to gene product relationship" -> "original subject" [color=blue, label="original subject", - lp="2407.5,221.5", - pos="e,2385.3,192.7 1842.2,251.96 1862.6,250.11 1883.7,248.37 1903.5,247 1997.8,240.5 2238.5,257.85 2328.5,229 2340.1,225.28 2341.2,220.57 \ -2351.5,214 2359.6,208.79 2368.5,203.21 2376.7,198.07", + lp="2444.5,221.5", + pos="e,2393.7,194.92 2484.3,258.83 2441.1,253.92 2402.4,244.98 2388.5,229 2382.2,221.83 2384,212.39 2388.4,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "gene to gene product relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2549,221.5", - pos="e,2504.9,195.49 1841.3,251.88 1862,250.01 1883.3,248.28 1903.5,247 1965.6,243.04 2405.5,251.62 2463.5,229 2471.2,225.98 2485.2,213.98 \ -2497.6,202.49", + lp="2572,221.5", + pos="e,2510.4,195.76 2554.5,249.65 2533.4,244.35 2515.1,237.52 2508.5,229 2503.2,222.16 2503.7,213.39 2506.5,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "gene to gene product relationship" -> "original object" [color=blue, label="original object", - lp="2678,221.5", - pos="e,2632.7,196.43 1840.8,251.8 1861.6,249.94 1883.2,248.22 1903.5,247 1942.9,244.62 2580.7,250.98 2613.5,229 2621.4,223.7 2626.5,214.89 \ -2629.7,206.12", + lp="2691,221.5", + pos="e,2636.9,196.18 2641.1,246.8 2640.1,235.16 2638.8,219.55 2637.7,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.5,178", + width=2.1304]; + "gene to gene product relationship" -> "subject category" [color=blue, + label="subject category", + lp="2817,221.5", + pos="e,2764.7,196.4 2714.2,248.69 2726,243.82 2737.3,237.42 2746.5,229 2753.2,222.84 2758,214.24 2761.4,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.5,178", + width=2.1304]; + "gene to gene product relationship" -> "object category" [color=blue, + label="object category", + lp="2960,221.5", + pos="e,2924.7,195.73 2763.1,252.42 2810.7,246.57 2859.1,238.65 2880.5,229 2894.1,222.83 2907.1,212.54 2917.4,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.5,178", + width=1.0652]; + "gene to gene product relationship" -> "subject closure" [color=blue, + label="subject closure", + lp="3096,221.5", + pos="e,3060.1,195.53 2763.1,252.4 2782.3,250.57 2801.9,248.72 2820.5,247 2864.7,242.89 2979,247.24 3019.5,229 3032.4,223.18 3044.2,212.87 \ +3053.3,203.13", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.5,178", + width=1.0652]; + "gene to gene product relationship" -> "object closure" [color=blue, + label="object closure", + lp="3216.5,221.5", + pos="e,3171.1,196.23 2760.2,252.06 2780.3,250.23 2801,248.46 2820.5,247 2857.5,244.23 3124.7,251.18 3154.5,229 3161.8,223.54 3166.2,214.8 \ +3168.8,206.15", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.5,178", + width=2.1304]; + "gene to gene product relationship" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3375,221.5", + pos="e,3298.5,196.11 2758.7,251.96 2779.3,250.1 2800.5,248.35 2820.5,247 2870.4,243.62 3226.6,252.99 3270.5,229 3280.3,223.67 3287.9,\ +214.3 3293.5,205.1", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.5,178", + width=2.1304]; + "gene to gene product relationship" -> "object category closure" [color=blue, + label="object category closure", + lp="3565,221.5", + pos="e,3491.8,196.1 2757.8,251.85 2778.6,249.97 2800.2,248.25 2820.5,247 2856.3,244.79 3435.4,246.9 3466.5,229 3475.7,223.71 3482.5,214.48 \ +3487.4,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.5,178", + width=1.0652]; + "gene to gene product relationship" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3737.5,221.5", + pos="e,3680.5,196.19 2757.3,251.78 2778.3,249.91 2800,248.2 2820.5,247 2866.6,244.3 3611.7,250.79 3652.5,229 3662.3,223.76 3670,214.4 \ +3675.6,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.5,178", + width=1.0652]; + "gene to gene product relationship" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.5,221.5", + pos="e,3839.1,195.73 2756.8,251.77 2778,249.88 2799.9,248.17 2820.5,247 2875.4,243.89 3760.6,254.18 3809.5,229 3819.8,223.68 3828,213.99 \ +3834,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.5,178", + width=1.0652]; + "gene to gene product relationship" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.5,221.5", + pos="e,3989.5,195.77 2756.8,251.73 2778,249.84 2799.9,248.15 2820.5,247 2852.1,245.25 3930.2,243.09 3958.5,229 3969.2,223.66 3977.8,213.84 \ +3984.3,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.5,178", + width=1.0652]; + "gene to gene product relationship" -> "object label closure" [color=blue, + label="object label closure", + lp="4216,221.5", + pos="e,4160.2,195.79 2756.3,251.74 2777.6,249.84 2799.7,248.13 2820.5,247 2856.8,245.02 4095.8,244.97 4128.5,229 4139.3,223.69 4148.2,\ +213.87 4154.8,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4321.5,178", + width=2.347]; + "gene to gene product relationship" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4375,221.5", + pos="e,4315.5,196.18 2756.3,251.71 2777.6,249.81 2799.7,248.12 2820.5,247 2861.2,244.81 4253.8,248.81 4289.5,229 4298.9,223.75 4306,214.39 \ +4311.1,205.18", style=solid]; type [height=0.5, - pos="2723.5,178", + pos="4455.5,178", width=0.86659]; "gene to gene product relationship" -> type [color=blue, label=type, - lp="2755.5,221.5", - pos="e,2733.3,195.51 1840.3,251.79 1861.3,249.91 1883,248.2 1903.5,247 1926.5,245.65 2717.4,245.48 2733.5,229 2739.7,222.66 2739.5,213.61 \ -2737,204.95", + lp="4473.5,221.5", + pos="e,4458.2,195.98 2756.3,251.69 2777.6,249.8 2799.7,248.1 2820.5,247 2843.1,245.8 4431.5,243.93 4448.5,229 4454.9,223.32 4457.5,214.65 \ +4458.2,206.12", style=solid]; category [height=0.5, - pos="2824.5,178", + pos="4556.5,178", width=1.4263]; "gene to gene product relationship" -> category [color=blue, label=category, - lp="2829,221.5", - pos="e,2813.4,195.84 1840.3,251.77 1861.3,249.89 1883,248.19 1903.5,247 1951.9,244.19 2731,248.23 2775.5,229 2787.9,223.65 2798.7,213.55 \ -2807,203.81", + lp="4552,221.5", + pos="e,4541.7,195.48 2756.3,251.69 2777.6,249.79 2799.7,248.1 2820.5,247 2866.9,244.54 4449.7,244.53 4493.5,229 4508.7,223.59 4523.1,\ +212.84 4534.2,202.68", style=solid]; subject [height=0.5, - pos="2938.5,178", + pos="4670.5,178", width=1.2277]; "gene to gene product relationship" -> subject [color=blue, label=subject, - lp="2921.5,221.5", - pos="e,2921.5,194.73 1839.8,251.78 1861,249.89 1882.9,248.18 1903.5,247 1956.8,243.96 2813.6,245.11 2864.5,229 2882.5,223.31 2900.1,211.72 \ -2913.6,201.13", + lp="4647.5,221.5", + pos="e,4651.7,194.32 2756.3,251.68 2777.6,249.78 2799.7,248.1 2820.5,247 2918.5,241.83 4493,255.77 4587.5,229 4607.6,223.29 4627.8,211.3 \ +4643.3,200.49", style=solid]; object [height=0.5, - pos="2981.5,91", + pos="4713.5,91", width=1.0832]; "gene to gene product relationship" -> object [color=blue, label=object, - lp="3024.5,178", - pos="e,2994.9,108.09 1839.8,251.75 1861,249.86 1882.9,248.16 1903.5,247 1961.6,243.73 2896.9,249.16 2951.5,229 2994,213.33 2999.2,186.96 \ -3004.5,142 3005.3,135.38 3006.4,133.39 3004.5,127 3003.5,123.55 3002,120.13 3000.2,116.85", + lp="4757.5,178", + pos="e,4726.9,108.09 2756.3,251.67 2777.6,249.77 2799.7,248.09 2820.5,247 2872,244.3 4628.5,245.03 4677.5,229 4701.4,221.18 4709.4,216.87 \ +4723.5,196 4737.3,175.52 4733.6,166.51 4736.5,142 4737.3,135.38 4738.4,133.39 4736.5,127 4735.5,123.55 4734,120.13 4732.2,116.85", style=solid]; predicate [height=0.5, - pos="3135.5,178", + pos="4867.5,178", width=1.5165]; "gene to gene product relationship" -> predicate [color=blue, label=predicate, - lp="3108.5,221.5", - pos="e,3111.6,194.3 1839.8,251.73 1861,249.84 1882.9,248.15 1903.5,247 2028.8,240.03 2910.4,258.08 3032.5,229 3057.4,223.07 3083.2,210.48 \ -3102.8,199.41", + lp="4840.5,221.5", + pos="e,4843.7,194.36 2756.3,251.66 2777.6,249.77 2799.7,248.09 2820.5,247 2928.3,241.36 4659.3,253.69 4764.5,229 4789.4,223.16 4815.3,\ +210.56 4834.9,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1950.5,265", + pos="2867.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2081.5,265", + pos="2998.5,265", width=2.0762]; subject -> object [label=relation, - lp="2976.5,134.5", - pos="e,2963.6,107.23 2939.6,159.55 2940.8,149.57 2943.3,137.07 2948.5,127 2950.7,122.68 2953.6,118.52 2956.8,114.66"]; + lp="4708.5,134.5", + pos="e,4695.6,107.23 4671.6,159.55 4672.8,149.57 4675.3,137.07 4680.5,127 4682.7,122.68 4685.6,118.52 4688.8,114.66"]; relation [height=0.5, - pos="2926.5,18", + pos="4658.5,18", width=1.2999]; - subject -> relation [pos="e,2927.8,36.188 2937.2,159.79 2935.1,132.48 2931,78.994 2928.6,46.38", + subject -> relation [pos="e,4659.8,36.188 4669.2,159.79 4667.1,132.48 4663,78.994 4660.6,46.38", style=dotted]; "gene to gene product relationship_subject" [color=blue, height=0.5, label=gene, - pos="2207.5,265", + pos="3124.5,265", width=0.92075]; - object -> relation [pos="e,2939.3,35.54 2969,73.889 2962.1,64.939 2953.3,53.617 2945.5,43.584", + object -> relation [pos="e,4671.3,35.54 4701,73.889 4694.1,64.939 4685.3,53.617 4677.5,43.584", style=dotted]; "gene to gene product relationship_object" [color=blue, height=0.5, label="gene product mixin", - pos="2359.5,265", + pos="3276.5,265", width=2.7984]; "gene to gene product relationship_predicate" [color=blue, height=0.5, label="predicate type", - pos="2556.5,265", + pos="3473.5,265", width=2.1665]; } diff --git a/graphviz/gene_to_gene_product_relationship.svg b/graphviz/gene_to_gene_product_relationship.svg index 68663b1298..0cca85e90b 100644 --- a/graphviz/gene_to_gene_product_relationship.svg +++ b/graphviz/gene_to_gene_product_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene product relationship - -gene to gene product relationship + +gene to gene product relationship @@ -24,9 +24,9 @@ gene to gene product relationship->sequence feature relationship - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to gene product relationship->id - - -id + + +id @@ -50,9 +50,9 @@ gene to gene product relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene product relationship->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene product relationship->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene product relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene product relationship->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene to gene product relationship->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to gene product relationship->publications - - -publications + + +publications @@ -141,9 +141,9 @@ gene to gene product relationship->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ gene to gene product relationship->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ gene to gene product relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ gene to gene product relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ gene to gene product relationship->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ gene to gene product relationship->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ gene to gene product relationship->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ gene to gene product relationship->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to gene product relationship->subject category + + +subject category + + + +object category + +ontology class + + + +gene to gene product relationship->object category + + +object category + + + +subject closure + +string + + + +gene to gene product relationship->subject closure + + +subject closure + + + +object closure + +string + + + +gene to gene product relationship->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to gene product relationship->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to gene product relationship->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to gene product relationship->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to gene product relationship->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to gene product relationship->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to gene product relationship->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to gene product relationship->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to gene product relationship->type - - -type + + +type - + category - -category + +category - + gene to gene product relationship->category - - -category + + +category - + subject - -subject + +subject - + gene to gene product relationship->subject - - -subject + + +subject - + object - -object + +object - + gene to gene product relationship->object - - -object + + +object - + predicate - -predicate + +predicate - + gene to gene product relationship->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to gene product relationship_subject - -gene + +gene - + object->relation - - + + - + gene to gene product relationship_object - -gene product mixin + +gene product mixin - + gene to gene product relationship_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_go_term_association.gv b/graphviz/gene_to_go_term_association.gv index 9af251c63e..c8ce6cae5b 100644 --- a/graphviz/gene_to_go_term_association.gv +++ b/graphviz/gene_to_go_term_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3162.8,283"]; + graph [bb="0,0,4886.8,283"]; node [label="\N"]; "gene to go term association" [height=0.5, label="gene to go term association", - pos="1640.8,265", + pos="2590.8,265", width=3.8816]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "gene to go term association" -> "functional association" [label=is_a, - lp="381.79,221.5", - pos="e,170.59,193.36 1501.7,263.08 1218.6,260.73 583.76,252.89 367.79,229 303.76,221.92 231.83,207.26 180.56,195.64"]; + lp="379.79,221.5", + pos="e,169.6,193.45 2451.4,263.26 1996.3,260.63 571.94,250.74 365.79,229 301.99,222.27 230.38,207.5 179.49,195.75"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to go term association" -> id [color=blue, label=id, - lp="501.79,221.5", - pos="e,308.51,189.94 1502.2,262.62 1241.2,259.55 685.84,250.64 494.79,229 419.61,220.48 400.75,216.02 327.79,196 324.64,195.13 321.39,\ -194.16 318.15,193.14", + lp="496.79,221.5", + pos="e,308.77,190 2451.5,263.17 2013.8,260.35 683.24,250.13 489.79,229 416.75,221.02 398.59,215.65 327.79,196 324.68,195.14 321.48,194.17 \ +318.28,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to go term association" -> iri [color=blue, label=iri, - lp="625.79,221.5", - pos="e,413.39,190.21 1503,261.73 1264.7,257.4 785.12,246.77 617.79,229 535.17,220.22 514.41,216.07 433.79,196 430.36,195.15 426.82,194.19 \ -423.28,193.17", + lp="613.79,221.5", + pos="e,413.69,190.23 2451.9,262.93 2031,259.51 787.59,247.9 605.79,229 528.37,220.95 509.21,215.26 433.79,196 430.41,195.14 426.93,194.18 \ +423.45,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to go term association" -> name [color=blue, label=name, - lp="734.79,221.5", - pos="e,539.77,190.85 1502.9,261.84 1283.1,257.87 862.89,248.04 714.79,229 657.31,221.61 592.72,205.5 549.47,193.56", + lp="725.79,221.5", + pos="e,538.41,191.15 2451.7,263.13 2045.2,260.33 877,250.52 705.79,229 650.97,222.11 589.61,206.11 548.22,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to go term association" -> description [color=blue, label=description, - lp="860.29,221.5", - pos="e,689,193.5 1502.7,262.17 1303.8,258.85 946.99,250.09 819.79,229 778.08,222.08 732.16,208.18 698.57,196.79", + lp="854.29,221.5", + pos="e,687.2,193.65 2451.3,263.47 2060.6,261.66 973.3,254.38 813.79,229 773.43,222.58 729.19,208.66 696.84,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to go term association" -> "has attribute" [color=blue, label="has attribute", - lp="1013.8,221.5", - pos="e,829.16,191.55 1505,260.65 1338.6,255.9 1066.6,245.86 966.79,229 922.42,221.5 873.25,206.5 838.88,194.88", + lp="1011.8,221.5", + pos="e,828.38,191.75 2451.8,263.11 2084.9,260.47 1109.3,251.4 964.79,229 920.66,222.16 871.91,207 837.97,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "gene to go term association" -> predicate [color=blue, label=predicate, - lp="1166.8,221.5", - pos="e,986.43,193 1503.6,261.54 1400.9,258.01 1257.3,249.49 1132.8,229 1086,221.3 1034,207.21 996.2,195.94", + lp="1172.8,221.5", + pos="e,986.21,193.09 2451,264.64 2138,265.43 1389.2,263.51 1138.8,229 1089.6,222.22 1034.9,207.65 995.79,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "gene to go term association" -> negated [color=blue, label=negated, - lp="1299.8,221.5", - pos="e,1120.1,190.34 1515.6,256.98 1443.6,251.74 1351.7,243.01 1270.8,229 1221.9,220.54 1167.3,204.99 1130.1,193.47", + lp="1318.8,221.5", + pos="e,1120.7,190.23 2451.4,263.61 2163.3,262.27 1510.9,256.21 1289.8,229 1234,222.13 1171.3,205.38 1130.4,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "gene to go term association" -> qualifiers [color=blue, label=qualifiers, - lp="1419.3,221.5", - pos="e,1266.5,193.53 1533.7,253.36 1487.8,247.76 1433.9,239.78 1385.8,229 1348.5,220.63 1307.3,207.57 1276.2,196.9", + lp="1455.3,221.5", + pos="e,1270,193.02 2451.3,263.68 2185.7,262.44 1616.5,256.53 1421.8,229 1373,222.11 1318.9,207.65 1280,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "gene to go term association" -> publications [color=blue, label=publications, - lp="1536.8,221.5", - pos="e,1412.8,194.2 1567.3,249.65 1543.3,244.15 1516.6,237.2 1492.8,229 1468.5,220.66 1442.4,208.78 1421.8,198.69", + lp="1597.8,221.5", + pos="e,1420.3,192.66 2451.3,263.64 2209.6,262.3 1722.3,256.17 1553.8,229 1510.9,222.09 1463.7,207.61 1429.9,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "gene to go term association" -> "has evidence" [color=blue, label="has evidence", - lp="1643.3,221.5", - pos="e,1559.5,195.6 1620.4,246.8 1605.1,233.96 1584.1,216.27 1567.3,202.19", + lp="1751.3,221.5", + pos="e,1577.8,193.55 2451.8,262.82 2239.4,260.28 1844.2,252.47 1704.8,229 1664.4,222.2 1620,208.38 1587.5,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "gene to go term association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1774.3,221.5", - pos="e,1727.1,196.14 1668.6,247.31 1677,241.84 1686,235.49 1693.8,229 1703,221.33 1712.3,212.07 1720.2,203.61", + lp="1901.3,221.5", + pos="e,1766.3,195.78 2450.9,264.75 2265.4,264.49 1948.5,259.38 1836.8,229 1815,223.09 1792.6,211.61 1775.1,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "gene to go term association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1982.8,221.5", - pos="e,1939.6,195.02 1734.1,251.54 1768.6,245.97 1807.7,238.49 1842.8,229 1872.4,220.97 1904.7,209.03 1930.2,198.83", + lp="2070.8,221.5", + pos="e,1971,196 2454.4,260.93 2278.2,256.29 1992,246.15 1975.8,229 1970,222.9 1968.8,214.27 1969.4,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "gene to go term association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2236.3,221.5", - pos="e,2178.2,195.2 1738.5,252.12 1755.6,250.25 1773.2,248.46 1789.8,247 1919.3,235.63 1954.7,256.66 2081.8,229 2111.9,222.45 2144.1,\ -210.06 2169,199.25", + lp="2279.3,221.5", + pos="e,2186,195.53 2453.4,261.58 2338.9,258.1 2191.8,249.62 2172.8,229 2165.1,220.62 2170,210.86 2178.5,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "gene to go term association" -> timepoint [color=blue, label=timepoint, - lp="2401.8,221.5", - pos="e,2383.3,195.77 1736.9,251.88 1754.4,249.99 1772.7,248.25 1789.8,247 1851.5,242.49 2290.4,254.49 2346.8,229 2358.8,223.56 2369.3,\ -213.44 2377.2,203.73", + lp="2430.8,221.5", + pos="e,2389.5,196.26 2473.6,255.18 2438.8,250.02 2407,241.87 2395.8,229 2390.4,222.83 2388.7,214.43 2388.7,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "gene to go term association" -> "original subject" [color=blue, label="original subject", - lp="2520.8,221.5", - pos="e,2488.6,194.22 1736.5,251.85 1754.2,249.96 1772.5,248.22 1789.8,247 1862,241.89 2372.6,253.25 2440.8,229 2449.6,225.86 2466.6,212.73 \ -2480.9,200.72", + lp="2528.8,221.5", + pos="e,2485.7,193.75 2500.9,251.13 2490,245.91 2480.1,238.76 2472.8,229 2466.1,220.01 2470.9,209.73 2478.7,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,204 @@ digraph { width=1.5887]; "gene to go term association" -> "original predicate" [color=blue, label="original predicate", - lp="2661.3,221.5", - pos="e,2611.2,196.24 1736.1,251.83 1753.9,249.92 1772.4,248.19 1789.8,247 1833.6,244.01 2540.4,248.47 2579.8,229 2590.5,223.72 2599.2,\ -214.09 2605.8,204.69", + lp="2655.3,221.5", + pos="e,2603,195.4 2588.5,246.84 2587.8,236.95 2588,224.45 2591.8,214 2593.1,210.42 2594.9,206.94 2597,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2751.8,178", + pos="2733.8,178", width=1.0652]; "gene to go term association" -> "original object" [color=blue, label="original object", - lp="2793.3,221.5", - pos="e,2748.8,195.98 1736.1,251.78 1753.9,249.87 1772.4,248.16 1789.8,247 1815.8,245.27 2707,243.28 2728.8,229 2736.9,223.68 2742.2,214.69 \ -2745.7,205.79", + lp="2780.3,221.5", + pos="e,2732.7,196.46 2682.3,251.35 2695.8,246.17 2708.6,238.98 2718.8,229 2724.9,223.04 2728.5,214.69 2730.7,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2866.8,178", + width=2.1304]; + "gene to go term association" -> "subject category" [color=blue, + label="subject category", + lp="2910.3,221.5", + pos="e,2860.6,196.16 2688.1,252.02 2753.7,243.63 2829.4,233.2 2835.8,229 2844.5,223.28 2851.3,214.13 2856.2,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3037.8,178", + width=2.1304]; + "gene to go term association" -> "object category" [color=blue, + label="object category", + lp="3055.3,221.5", + pos="e,3021.9,195.85 2689.7,252.2 2706.4,250.35 2723.6,248.55 2739.8,247 2791.7,242.04 2925.2,247.86 2973.8,229 2988.7,223.22 3003,212.74 \ +3014.2,202.86", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3170.8,178", + width=1.0652]; + "gene to go term association" -> "subject closure" [color=blue, + label="subject closure", + lp="3192.3,221.5", + pos="e,3158,195.26 2687.7,252.01 2705,250.13 2722.9,248.37 2739.8,247 2781.4,243.63 3076.2,244.8 3114.8,229 3128.6,223.34 3141.3,212.7 \ +3151.1,202.69", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3270.8,178", + width=1.0652]; + "gene to go term association" -> "object closure" [color=blue, + label="object closure", + lp="3312.8,221.5", + pos="e,3268.7,196.35 2686.9,251.92 2704.5,250.03 2722.7,248.28 2739.8,247 2768.1,244.89 3227.6,245.34 3250.8,229 3258.5,223.61 3263.2,\ +214.77 3266.1,206.01", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3403.8,178", + width=2.1304]; + "gene to go term association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3471.3,221.5", + pos="e,3396.1,196.18 2686.5,251.87 2704.2,249.97 2722.5,248.23 2739.8,247 2774.5,244.52 3335.9,245.13 3366.8,229 3376.9,223.7 3385,214.2 \ +3391,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3595.8,178", + width=2.1304]; + "gene to go term association" -> "object category closure" [color=blue, + label="object category closure", + lp="3662.3,221.5", + pos="e,3589.5,196.16 2686.1,251.81 2703.9,249.91 2722.4,248.18 2739.8,247 2785.4,243.9 3522.8,251.11 3562.8,229 3572.3,223.72 3579.6,\ +214.36 3584.9,205.15", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3785.8,178", + width=1.0652]; + "gene to go term association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3834.8,221.5", + pos="e,3778.7,195.72 2686.1,251.76 2703.9,249.86 2722.4,248.15 2739.8,247 2795.8,243.31 3700.1,255.03 3749.8,229 3760,223.66 3768,213.98 \ +3773.8,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3944.8,178", + width=1.0652]; + "gene to go term association" -> "object namespace" [color=blue, + label="object namespace", + lp="3988.8,221.5", + pos="e,3937.1,195.76 2685.7,251.77 2703.6,249.85 2722.3,248.13 2739.8,247 2772.1,244.91 3877.9,243.63 3906.8,229 3917.3,223.71 3925.6,\ +214.03 3931.8,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4095.8,178", + width=1.0652]; + "gene to go term association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4148.8,221.5", + pos="e,4087.8,195.78 2685.6,251.74 2703.6,249.83 2722.3,248.12 2739.8,247 2776.3,244.67 4024,245.28 4056.8,229 4067.5,223.68 4076.2,213.86 \ +4082.6,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4266.8,178", + width=1.0652]; + "gene to go term association" -> "object label closure" [color=blue, + label="object label closure", + lp="4314.3,221.5", + pos="e,4258.5,195.8 2685.6,251.72 2703.6,249.81 2722.3,248.1 2739.8,247 2781,244.41 4189.7,247.12 4226.8,229 4237.7,223.7 4246.5,213.88 \ +4253.1,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4428.8,178", + width=2.347]; + "gene to go term association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4477.3,221.5", + pos="e,4419.9,196.31 2685.6,251.7 2703.6,249.79 2722.2,248.09 2739.8,247 2785.5,244.15 4346.5,248.81 4387.8,229 4398.6,223.79 4407.6,\ +214.18 4414.3,204.77", style=solid]; type [height=0.5, - pos="2839.8,178", + pos="4562.8,178", width=0.86659]; "gene to go term association" -> type [color=blue, label=type, - lp="2870.8,221.5", - pos="e,2849.2,195.54 1736.1,251.75 1753.9,249.85 1772.4,248.14 1789.8,247 1819.1,245.08 2828.2,249.98 2848.8,229 2855,222.69 2855,213.66 \ -2852.6,205", + lp="4576.8,221.5", + pos="e,4563.6,196.18 2685.2,251.73 2703.3,249.8 2722.1,248.09 2739.8,247 2764.9,245.45 4531.1,244.67 4550.8,229 4557.6,223.54 4561,214.93 \ +4562.5,206.37", style=solid]; category [height=0.5, - pos="2940.8,178", + pos="4663.8,178", width=1.4263]; "gene to go term association" -> category [color=blue, label=category, - lp="2945.3,221.5", - pos="e,2929.4,195.87 1735.7,251.78 1753.6,249.86 1772.3,248.14 1789.8,247 1850.8,243.03 2834.5,252.87 2890.8,229 2903.3,223.69 2914.4,\ -213.59 2922.9,203.85", + lp="4657.3,221.5", + pos="e,4648.2,195.25 2685.2,251.73 2703.3,249.8 2722.1,248.09 2739.8,247 2791.3,243.82 4547.9,245.49 4596.8,229 4613,223.53 4628.5,212.51 \ +4640.5,202.2", style=solid]; subject [height=0.5, - pos="3054.8,178", + pos="4777.8,178", width=1.2277]; "gene to go term association" -> subject [color=blue, label=subject, - lp="3037.8,221.5", - pos="e,3037.8,194.76 1735.7,251.76 1753.6,249.85 1772.3,248.13 1789.8,247 1855.8,242.74 2917.7,248.85 2980.8,229 2998.8,223.34 3016.4,\ -211.75 3029.9,201.16", + lp="4753.8,221.5", + pos="e,4758.5,194.33 2685.2,251.72 2703.3,249.8 2722.1,248.09 2739.8,247 2848.1,240.34 4588.2,257.99 4692.8,229 4713.5,223.25 4734.4,\ +211.09 4750.3,200.2", style=solid]; object [height=0.5, - pos="3097.8,91", + pos="4820.8,91", width=1.0832]; "gene to go term association" -> object [color=blue, label=object, - lp="3140.8,178", - pos="e,3111.2,108.09 1735.6,251.75 1753.6,249.83 1772.3,248.12 1789.8,247 1860.7,242.47 3001.1,253.48 3067.8,229 3110.3,213.39 3115.5,\ -186.96 3120.8,142 3121.6,135.38 3122.7,133.39 3120.8,127 3119.8,123.55 3118.3,120.13 3116.5,116.85", + lp="4864.8,178", + pos="e,4834.2,108.09 2685.2,251.71 2703.3,249.79 2722.1,248.08 2739.8,247 2796.5,243.53 4729.7,246.35 4783.8,229 4808.1,221.2 4816.4,\ +217.1 4830.8,196 4844.7,175.59 4840.9,166.51 4843.8,142 4844.6,135.38 4845.7,133.39 4843.8,127 4842.8,123.55 4841.3,120.13 4839.5,\ +116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1836.8,265", + pos="2786.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1967.8,265", + pos="2917.8,265", width=2.0762]; subject -> object [label=relation, - lp="3092.8,134.5", - pos="e,3079.9,107.23 3055.9,159.55 3057.1,149.57 3059.6,137.07 3064.8,127 3067,122.68 3069.9,118.52 3073.1,114.66"]; + lp="4815.8,134.5", + pos="e,4802.9,107.23 4778.9,159.55 4780.1,149.57 4782.6,137.07 4787.8,127 4790,122.68 4792.9,118.52 4796.1,114.66"]; relation [height=0.5, - pos="3042.8,18", + pos="4765.8,18", width=1.2999]; - subject -> relation [pos="e,3044.1,36.188 3053.5,159.79 3051.4,132.48 3047.3,78.994 3044.9,46.38", + subject -> relation [pos="e,4767.1,36.188 4776.5,159.79 4774.4,132.48 4770.3,78.994 4767.9,46.38", style=dotted]; "gene to go term association_subject" [color=blue, height=0.5, label=gene, - pos="2093.8,265", + pos="3043.8,265", width=0.92075]; - object -> relation [pos="e,3055.6,35.54 3085.3,73.889 3078.4,64.939 3069.6,53.617 3061.8,43.584", + object -> relation [pos="e,4778.6,35.54 4808.3,73.889 4801.4,64.939 4792.6,53.617 4784.8,43.584", style=dotted]; "gene to go term association_object" [color=blue, height=0.5, label="ontology class", - pos="2221.8,265", + pos="3171.8,265", width=2.1304]; } diff --git a/graphviz/gene_to_go_term_association.svg b/graphviz/gene_to_go_term_association.svg index 9a220f26b9..59c4d04d03 100644 --- a/graphviz/gene_to_go_term_association.svg +++ b/graphviz/gene_to_go_term_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to go term association - -gene to go term association + +gene to go term association @@ -24,9 +24,9 @@ gene to go term association->functional association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to go term association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to go term association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to go term association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to go term association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to go term association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to go term association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ gene to go term association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ gene to go term association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ gene to go term association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ gene to go term association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ gene to go term association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ gene to go term association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ gene to go term association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ gene to go term association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ gene to go term association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ gene to go term association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to go term association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to go term association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to go term association->object category + + +object category + + + +subject closure + +string + + + +gene to go term association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to go term association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to go term association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to go term association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to go term association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to go term association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to go term association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to go term association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to go term association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to go term association->type - - -type + + +type - + category - -category + +category - + gene to go term association->category - - -category + + +category - + subject - -subject + +subject - + gene to go term association->subject - - -subject + + +subject - + object - -object + +object - + gene to go term association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to go term association_subject - -gene + +gene - + object->relation - - + + - + gene to go term association_object - -ontology class + +ontology class diff --git a/graphviz/gene_to_pathway_association.gv b/graphviz/gene_to_pathway_association.gv index b9dc9f42be..9179542437 100644 --- a/graphviz/gene_to_pathway_association.gv +++ b/graphviz/gene_to_pathway_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3401.4,283"]; + graph [bb="0,0,5125.4,283"]; node [label="\N"]; "gene to pathway association" [height=0.5, label="gene to pathway association", - pos="1778.4,265", + pos="2761.4,265", width=3.9538]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to pathway association" -> association [label=is_a, - lp="476.39,221.5", - pos="e,107.53,190.62 1636.1,263.65 1394.5,262.28 888.93,256.09 462.39,229 316.18,219.71 278.89,220.22 134.39,196 128.93,195.08 123.27,\ -193.99 117.62,192.82"]; + lp="467.39,221.5", + pos="e,107.53,190.6 2619.4,263.48 2185,261.65 877.94,254.13 453.39,229 311.11,220.58 274.93,219.76 134.39,196 128.93,195.08 123.27,193.98 \ +117.62,192.8"]; "gene to entity association mixin" [height=0.5, pos="302.39,178", width=4.4232]; "gene to pathway association" -> "gene to entity association mixin" [label=uses, - lp="617.89,221.5", - pos="e,375.14,194.01 1637.6,262.21 1370.3,258.42 798.3,248.3 601.39,229 527.86,221.79 445.07,207.45 385.28,195.97"]; + lp="615.89,221.5", + pos="e,373.72,194.11 2618.8,264.5 2202.5,265.5 993.08,265.12 599.39,229 525.93,222.26 443.23,207.76 383.79,196.11"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "gene to pathway association" -> id [color=blue, label=id, - lp="740.39,221.5", - pos="e,547.11,189.94 1637.6,262.1 1394.1,258.36 904.15,248.6 733.39,229 658.23,220.37 639.36,216.02 566.39,196 563.24,195.13 559.99,194.16 \ -556.75,193.14", + lp="735.39,221.5", + pos="e,547.38,190 2619.9,263.07 2189.5,260.03 914.59,249.39 728.39,229 655.35,221 637.2,215.65 566.39,196 563.29,195.14 560.09,194.17 \ +556.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "gene to pathway association" -> iri [color=blue, label=iri, - lp="862.39,221.5", - pos="e,652,190.2 1635.9,264.84 1454,264.48 1129.9,259.04 854.39,229 772.67,220.09 752.15,215.93 672.39,196 668.96,195.14 665.43,194.18 \ -661.89,193.17", + lp="852.39,221.5", + pos="e,652.29,190.23 2619.1,264.56 2235.9,265.57 1188.2,264.85 844.39,229 766.98,220.93 747.81,215.26 672.39,196 669.02,195.14 665.54,\ +194.18 662.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "gene to pathway association" -> name [color=blue, label=name, - lp="970.39,221.5", - pos="e,778.2,190.89 1639.2,261.15 1438.9,256.53 1079.3,246.15 950.39,229 894,221.5 830.68,205.55 788.04,193.67", + lp="964.39,221.5", + pos="e,777.39,191.26 2619.9,263 2221.5,259.95 1108.4,249.67 944.39,229 889.75,222.11 828.59,206.19 787.21,194.15", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "gene to pathway association" -> description [color=blue, label=description, - lp="1094.9,221.5", - pos="e,926.99,193.56 1639,261.31 1461,257.16 1162.8,247.66 1054.4,229 1013.9,222.04 969.47,208.3 936.75,196.99", + lp="1092.9,221.5", + pos="e,925.8,193.64 2619.4,263.33 2237.1,261.22 1204.7,253.3 1052.4,229 1012,222.56 967.8,208.65 935.45,197.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "gene to pathway association" -> "has attribute" [color=blue, label="has attribute", - lp="1246.4,221.5", - pos="e,1067.2,191.7 1636,264.56 1518.2,262.84 1346.7,255.28 1199.4,229 1157,221.43 1110.1,206.69 1077,195.16", + lp="1250.4,221.5", + pos="e,1067,191.74 2619.8,262.95 2262.1,259.98 1340.8,250.36 1203.4,229 1159.3,222.14 1110.5,206.98 1076.6,195.14", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "gene to pathway association" -> predicate [color=blue, label=predicate, - lp="1396.4,221.5", - pos="e,1224,193.2 1644.1,259.03 1562.2,254.43 1455.7,245.66 1362.4,229 1318.4,221.14 1269.6,207.36 1233.8,196.25", + lp="1410.4,221.5", + pos="e,1224.6,193.08 2619,264.47 2315.3,264.81 1612.8,261.87 1376.4,229 1327.6,222.22 1273.5,207.75 1234.6,196.12", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "gene to pathway association" -> negated [color=blue, label=negated, - lp="1518.4,221.5", - pos="e,1359.6,189.93 1662.3,254.52 1609.3,249.01 1545.8,240.78 1489.4,229 1439.4,218.56 1428.2,210.87 1379.4,196 1376.1,194.99 1372.7,\ -193.95 1369.2,192.9", + lp="1555.4,221.5", + pos="e,1359,190.21 2619.5,263.41 2341.5,261.69 1733.8,254.98 1526.4,229 1471.1,222.07 1409.1,205.34 1368.5,193.13", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "gene to pathway association" -> qualifiers [color=blue, label=qualifiers, - lp="1626.9,221.5", - pos="e,1499.3,194.24 1690.6,250.82 1659.6,245.27 1624.7,237.98 1593.4,229 1564.5,220.71 1533.1,208.5 1508.7,198.21", + lp="1690.9,221.5", + pos="e,1507.9,193 2619.6,263.44 2364.7,261.77 1838.8,255.16 1657.4,229 1609.4,222.07 1556,207.62 1517.8,196.03", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "gene to pathway association" -> publications [color=blue, label=publications, - lp="1730.4,221.5", - pos="e,1640.4,195.45 1728.5,248.11 1714.5,242.83 1699.5,236.39 1686.4,229 1673,221.42 1659.3,211.19 1648.1,201.95", + lp="1831.4,221.5", + pos="e,1658.1,192.76 2619.4,263.39 2388.8,261.65 1943,254.93 1787.4,229 1746.1,222.11 1700.6,207.8 1667.9,196.25", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "gene to pathway association" -> "has evidence" [color=blue, label="has evidence", - lp="1824.9,221.5", - pos="e,1778.4,196.18 1778.4,246.8 1778.4,235.16 1778.4,219.55 1778.4,206.24", + lp="1982.9,221.5", + pos="e,1815.4,193.77 2620,262.5 2419.7,259.6 2063.5,251.39 1936.4,229 1898,222.24 1856.1,208.65 1825,197.35", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "gene to pathway association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1972.9,221.5", - pos="e,1948.1,195.37 1825.6,248.01 1841.6,242.33 1859.4,235.69 1875.4,229 1896.7,220.11 1919.9,209.19 1939.1,199.83", + lp="2128.9,221.5", + pos="e,2001.8,195.77 2618.9,264.91 2445.7,264.61 2164.4,259.21 2064.4,229 2045.1,223.17 2025.6,212 2010.3,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "gene to pathway association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2195.4,221.5", - pos="e,2169,194.37 1878.7,252.2 1939.5,244.75 2011,235.36 2041.4,229 2081.3,220.66 2125.4,207.94 2159.3,197.41", + lp="2296.4,221.5", + pos="e,2203.3,196.25 2624.4,260.09 2463.2,254.8 2215.7,244.25 2201.4,229 2195.4,222.6 2196,213.84 2199,205.44", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,9 +147,8 @@ digraph { width=3.015]; "gene to pathway association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2457.9,221.5", - pos="e,2410.7,194.89 1877.2,252.05 1894.9,250.16 1913.2,248.39 1930.4,247 2091.8,233.99 2135,257.96 2294.4,229 2331,222.35 2370.9,209.43 \ -2401.2,198.4", + lp="2504.9,221.5", + pos="e,2416.3,195.1 2625.5,259.6 2529,255.02 2413.9,246.05 2398.4,229 2389.6,219.36 2396.6,209.3 2407.9,200.75", style=solid]; timepoint [color=blue, height=0.5, @@ -159,9 +157,8 @@ digraph { width=1.5346]; "gene to pathway association" -> timepoint [color=blue, label=timepoint, - lp="2631.4,221.5", - pos="e,2617.3,195.39 1876,251.87 1894.1,249.97 1912.8,248.23 1930.4,247 2001.1,242.05 2501.7,253.03 2568.4,229 2583.9,223.41 2598.6,212.49 \ -2610,202.27", + lp="2654.4,221.5", + pos="e,2621.3,195.8 2671.6,250.98 2647.9,245.61 2626.8,238.39 2619.4,229 2614.1,222.2 2614.6,213.44 2617.3,205.16", style=solid]; "original subject" [color=blue, height=0.5, @@ -170,9 +167,8 @@ digraph { width=1.0652]; "gene to pathway association" -> "original subject" [color=blue, label="original subject", - lp="2757.4,221.5", - pos="e,2727.7,194.46 1876,251.81 1894.1,249.92 1912.8,248.2 1930.4,247 2012.5,241.42 2592,254.03 2670.4,229 2688.5,223.22 2706.2,211.51 \ -2719.8,200.88", + lp="2751.4,221.5", + pos="e,2718.3,191.31 2715.2,247.95 2707.3,243.1 2700.1,236.89 2695.4,229 2688.1,216.95 2697.5,205.59 2709.8,196.74", style=solid]; "original predicate" [color=blue, height=0.5, @@ -181,85 +177,203 @@ digraph { width=1.5887]; "gene to pathway association" -> "original predicate" [color=blue, label="original predicate", - lp="2898.9,221.5", - pos="e,2849.5,196.27 1875.6,251.8 1893.8,249.89 1912.6,248.17 1930.4,247 1979.6,243.76 2773.1,250.53 2817.4,229 2828.2,223.74 2837.2,\ -214.12 2843.9,204.71", + lp="2886.9,221.5", + pos="e,2842.4,195.75 2784.8,247.1 2792.2,241.53 2800.3,235.17 2807.4,229 2816.8,220.85 2826.7,211.38 2835.2,202.9", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2990.4,178", + pos="2972.4,178", width=1.0652]; "gene to pathway association" -> "original object" [color=blue, label="original object", - lp="3030.9,221.5", - pos="e,2987.1,196.01 1875.2,251.8 1893.5,249.88 1912.5,248.15 1930.4,247 1959.1,245.15 2942.2,244.54 2966.4,229 2974.7,223.66 2980.2,\ -214.54 2983.8,205.54", + lp="3016.9,221.5", + pos="e,2970.6,196.32 2871.5,253.58 2907.1,248.21 2941,240.33 2954.4,229 2961.2,223.24 2965.4,214.7 2968.1,206.3", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3105.4,178", + width=2.1304]; + "gene to pathway association" -> "subject category" [color=blue, + label="subject category", + lp="3147.9,221.5", + pos="e,3098.6,196.3 2864.4,252.47 2954.8,242.34 3072.1,229.17 3072.4,229 3081.5,223.43 3088.6,214.32 3093.8,205.38", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3276.4,178", + width=2.1304]; + "gene to pathway association" -> "object category" [color=blue, + label="object category", + lp="3292.9,221.5", + pos="e,3260.5,195.7 2861.1,252.12 2878.5,250.25 2896.5,248.46 2913.4,247 2979.5,241.31 3149.3,252.25 3211.4,229 3226.8,223.24 3241.5,\ +212.52 3253,202.48", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3409.4,178", + width=1.0652]; + "gene to pathway association" -> "subject closure" [color=blue, + label="subject closure", + lp="3429.9,221.5", + pos="e,3396.3,195.29 2859.8,251.97 2877.6,250.08 2896.1,248.32 2913.4,247 2962.1,243.28 3307.1,247.13 3352.4,229 3366.4,223.39 3379.3,\ +212.76 3389.3,202.74", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3509.4,178", + width=1.0652]; + "gene to pathway association" -> "object closure" [color=blue, + label="object closure", + lp="3551.4,221.5", + pos="e,3506.9,196.38 2859.4,251.87 2877.3,249.98 2895.9,248.25 2913.4,247 2945.3,244.72 3462.1,247.1 3488.4,229 3496.2,223.65 3501.1,\ +214.82 3504.2,206.06", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3642.4,178", + width=2.1304]; + "gene to pathway association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3709.9,221.5", + pos="e,3634.7,196.2 2859,251.84 2877.1,249.94 2895.8,248.21 2913.4,247 2951.8,244.36 3571.3,246.75 3605.4,229 3615.6,223.71 3623.7,214.22 \ +3629.6,204.91", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3834.4,178", + width=2.1304]; + "gene to pathway association" -> "object category closure" [color=blue, + label="object category closure", + lp="3900.9,221.5", + pos="e,3828.1,196.16 2858.6,251.8 2876.8,249.89 2895.6,248.17 2913.4,247 2962.6,243.75 3758.2,252.82 3801.4,229 3811,223.73 3818.2,214.37 \ +3823.5,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4024.4,178", + width=1.0652]; + "gene to pathway association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4073.4,221.5", + pos="e,4017.3,195.73 2858.2,251.79 2876.5,249.87 2895.5,248.15 2913.4,247 2943.2,245.09 3961.9,242.84 3988.4,229 3998.6,223.67 4006.6,\ +213.98 4012.4,204.55", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4183.4,178", + width=1.0652]; + "gene to pathway association" -> "object namespace" [color=blue, + label="object namespace", + lp="4227.4,221.5", + pos="e,4175.7,195.76 2858.2,251.76 2876.5,249.84 2895.5,248.13 2913.4,247 2947.6,244.85 4114.8,244.43 4145.4,229 4155.9,223.71 4164.2,\ +214.03 4170.4,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4334.4,178", + width=1.0652]; + "gene to pathway association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4387.4,221.5", + pos="e,4326.4,195.78 2858.2,251.73 2876.5,249.82 2895.5,248.11 2913.4,247 2951.7,244.61 4261,246.07 4295.4,229 4306.1,223.68 4314.8,213.86 \ +4321.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4505.4,178", + width=1.0652]; + "gene to pathway association" -> "object label closure" [color=blue, + label="object label closure", + lp="4553.9,221.5", + pos="e,4497.1,195.8 2858.2,251.71 2876.5,249.8 2895.5,248.1 2913.4,247 2956.4,244.35 4426.6,247.9 4465.4,229 4476.3,223.7 4485.1,213.89 \ +4491.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4667.4,178", + width=2.347]; + "gene to pathway association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4715.9,221.5", + pos="e,4658.8,196.3 2857.8,251.74 2876.2,249.81 2895.4,248.1 2913.4,247 2960.9,244.1 4584.6,249.85 4627.4,229 4638.1,223.78 4646.9,214.17 \ +4653.4,204.75", style=solid]; type [height=0.5, - pos="3078.4,178", + pos="4801.4,178", width=0.86659]; "gene to pathway association" -> type [color=blue, label=type, - lp="3108.4,221.5", - pos="e,3087.4,195.57 1875.2,251.77 1893.5,249.86 1912.5,248.14 1930.4,247 1962.4,244.96 3063.9,251.88 3086.4,229 3092.5,222.79 3092.7,\ -213.88 3090.6,205.3", + lp="4815.4,221.5", + pos="e,4802.2,196.19 2857.8,251.73 2876.2,249.8 2895.4,248.09 2913.4,247 2939.4,245.42 4769,245.23 4789.4,229 4796.2,223.54 4799.6,214.93 \ +4801.2,206.37", style=solid]; category [height=0.5, - pos="3179.4,178", + pos="4902.4,178", width=1.4263]; "gene to pathway association" -> category [color=blue, label=category, - lp="3182.9,221.5", - pos="e,3167.7,195.88 1875.2,251.76 1893.5,249.85 1912.5,248.13 1930.4,247 1996.8,242.8 3067,254.63 3128.4,229 3141.2,223.65 3152.6,213.41 \ -3161.3,203.57", + lp="4895.9,221.5", + pos="e,4886.8,195.26 2857.8,251.72 2876.2,249.8 2895.4,248.09 2913.4,247 2966.7,243.78 4784.8,246.06 4835.4,229 4851.6,223.54 4867.1,\ +212.51 4879.1,202.2", style=solid]; subject [height=0.5, - pos="3293.4,178", + pos="5016.4,178", width=1.2277]; "gene to pathway association" -> subject [color=blue, label=subject, - lp="3276.4,221.5", - pos="e,3276.1,194.77 1875.2,251.75 1893.5,249.84 1912.5,248.12 1930.4,247 2001.8,242.52 3150,250.22 3218.4,229 3236.6,223.35 3254.4,211.77 \ -3268.2,201.17", + lp="4992.4,221.5", + pos="e,4997.1,194.33 2857.8,251.72 2876.2,249.79 2895.4,248.09 2913.4,247 3025.3,240.26 4823.4,258.94 4931.4,229 4952.1,223.25 4973,211.09 \ +4988.9,200.2", style=solid]; object [height=0.5, - pos="3336.4,91", + pos="5059.4,91", width=1.0832]; "gene to pathway association" -> object [color=blue, label=object, - lp="3379.4,178", - pos="e,3349.8,108.09 1875.2,251.74 1893.5,249.82 1912.5,248.11 1930.4,247 2006.7,242.25 3234.6,255.32 3306.4,229 3348.9,213.41 3354.1,\ -186.96 3359.4,142 3360.2,135.38 3361.3,133.39 3359.4,127 3358.4,123.55 3356.9,120.13 3355.1,116.85", + lp="5103.4,178", + pos="e,5072.8,108.09 2857.8,251.71 2876.2,249.79 2895.4,248.08 2913.4,247 2971.9,243.49 4966.6,246.89 5022.4,229 5046.7,221.21 5055,217.1 \ +5069.4,196 5083.3,175.59 5079.5,166.51 5082.4,142 5083.2,135.38 5084.3,133.39 5082.4,127 5081.4,123.55 5079.9,120.13 5078.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1977.4,265", + pos="2960.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2108.4,265", + pos="3091.4,265", width=2.0762]; subject -> object [label=relation, - lp="3331.4,134.5", - pos="e,3318.5,107.23 3294.5,159.55 3295.7,149.57 3298.2,137.07 3303.4,127 3305.6,122.68 3308.5,118.52 3311.7,114.66"]; + lp="5054.4,134.5", + pos="e,5041.5,107.23 5017.5,159.55 5018.7,149.57 5021.2,137.07 5026.4,127 5028.6,122.68 5031.5,118.52 5034.7,114.66"]; relation [height=0.5, - pos="3281.4,18", + pos="5004.4,18", width=1.2999]; - subject -> relation [pos="e,3282.7,36.188 3292.1,159.79 3290,132.48 3286,78.994 3283.5,46.38", + subject -> relation [pos="e,5005.7,36.188 5015.1,159.79 5013,132.48 5009,78.994 5006.5,46.38", style=dotted]; "gene to pathway association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2311.4,265", + pos="3294.4,265", width=3.0692]; - object -> relation [pos="e,3294.2,35.54 3323.9,73.889 3317,64.939 3308.2,53.617 3300.4,43.584", + object -> relation [pos="e,5017.2,35.54 5046.9,73.889 5040,64.939 5031.2,53.617 5023.4,43.584", style=dotted]; "gene to pathway association_object" [color=blue, height=0.5, label=pathway, - pos="2490.4,265", + pos="3473.4,265", width=1.3902]; } diff --git a/graphviz/gene_to_pathway_association.svg b/graphviz/gene_to_pathway_association.svg index 4e38c55d1b..3db14ac7c7 100644 --- a/graphviz/gene_to_pathway_association.svg +++ b/graphviz/gene_to_pathway_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to pathway association - -gene to pathway association + +gene to pathway association @@ -24,9 +24,9 @@ gene to pathway association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to pathway association->gene to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ gene to pathway association->id - - -id + + +id @@ -63,9 +63,9 @@ gene to pathway association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ gene to pathway association->name - - -name + + +name @@ -89,9 +89,9 @@ gene to pathway association->description - - -description + + +description @@ -102,9 +102,9 @@ gene to pathway association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ gene to pathway association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ gene to pathway association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ gene to pathway association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ gene to pathway association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ gene to pathway association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ gene to pathway association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ gene to pathway association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ gene to pathway association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ gene to pathway association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ gene to pathway association->original subject - - -original subject + + +original subject @@ -245,123 +245,266 @@ gene to pathway association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to pathway association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to pathway association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to pathway association->object category + + +object category + + + +subject closure + +string + + + +gene to pathway association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to pathway association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to pathway association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to pathway association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to pathway association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to pathway association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to pathway association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to pathway association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to pathway association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to pathway association->type - - -type + + +type - + category - -category + +category - + gene to pathway association->category - - -category + + +category - + subject - -subject + +subject - + gene to pathway association->subject - - -subject + + +subject - + object - -object + +object - + gene to pathway association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to pathway association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene to pathway association_object - -pathway + +pathway diff --git a/graphviz/gene_to_phenotypic_feature_association.gv b/graphviz/gene_to_phenotypic_feature_association.gv index 2f52f86f9f..cc2b6f59df 100644 --- a/graphviz/gene_to_phenotypic_feature_association.gv +++ b/graphviz/gene_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4932.4,283"]; + graph [bb="0,0,6616.4,283"]; node [label="\N"]; "gene to phenotypic feature association" [height=0.5, label="gene to phenotypic feature association", - pos="2957.4,265", + pos="3709.4,265", width=5.2898]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to phenotypic feature association" -> association [label=is_a, lp="701.39,221.5", - pos="e,106.72,190.73 2767.1,263.9 2377,263.08 1458.1,257.92 687.39,229 441.35,219.77 378,231.76 134.39,196 128.61,195.15 122.62,194.07 \ + pos="e,106.72,190.73 3520,263 2947.9,259.79 1242.7,248.77 687.39,229 441.34,220.24 378,231.76 134.39,196 128.61,195.15 122.62,194.07 \ 116.66,192.86"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "gene to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="930.89,221.5", - pos="e,491.58,192.99 2768.4,262.55 2333.4,258.93 1271.5,248.35 914.39,229 773.35,221.36 612.39,205.82 501.79,194.08"]; + pos="e,490.75,193.07 3519.4,263.57 2976.2,262.03 1423,255.39 914.39,229 772.98,221.66 611.59,206.02 500.96,194.17"]; "gene to entity association mixin" [height=0.5, pos="768.39,178", width=4.4232]; "gene to phenotypic feature association" -> "gene to entity association mixin" [label=uses, lp="1081.9,221.5", - pos="e,840.02,194.13 2767,264.07 2354.8,263.62 1391.1,259.26 1065.4,229 992.06,222.19 909.52,207.73 850.1,196.11"]; + pos="e,839.41,194.11 3519.9,263.18 2955.1,260.48 1307.2,250.83 1065.4,229 991.8,222.36 908.95,207.81 849.49,196.11"]; id [color=blue, height=0.5, label=string, @@ -31,8 +31,8 @@ digraph { width=1.0652]; "gene to phenotypic feature association" -> id [color=blue, label=id, - lp="1202.4,221.5", - pos="e,1013.4,190 2766.8,264.54 2375.8,264.95 1494.8,262.01 1195.4,229 1121.9,220.9 1103.6,215.72 1032.4,196 1029.3,195.14 1026.1,194.18 \ + lp="1201.4,221.5", + pos="e,1013.4,190 3519.5,263.41 2973.3,261.41 1422.7,253.62 1194.4,229 1121.3,221.12 1103.2,215.65 1032.4,196 1029.3,195.14 1026.1,194.17 \ 1022.9,193.16", style=solid]; iri [color=blue, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "gene to phenotypic feature association" -> iri [color=blue, label=iri, - lp="1320.4,221.5", - pos="e,1118,190.15 2767.1,263.92 2396.3,263.12 1588.9,257.96 1312.4,229 1234.1,220.8 1214.7,215.39 1138.4,196 1135,195.13 1131.4,194.16 \ -1127.9,193.14", + lp="1318.4,221.5", + pos="e,1118.3,190.23 3519.8,263.14 2991.5,260.49 1527.1,251.2 1310.4,229 1233,221.07 1213.8,215.26 1138.4,196 1135,195.14 1131.5,194.18 \ +1128,193.17", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "gene to phenotypic feature association" -> name [color=blue, label=name, - lp="1432.4,221.5", - pos="e,1243.4,191.11 2767,264.57 2413.6,264.83 1668.7,261.33 1412.4,229 1357,222.01 1294.8,205.97 1253.1,193.93", + lp="1429.4,221.5", + pos="e,1243.2,191.3 3519.3,263.48 3005.9,261.75 1615.5,254.72 1409.4,229 1355,222.21 1294.1,206.27 1253,194.2", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "gene to phenotypic feature association" -> description [color=blue, label=description, - lp="1560.9,221.5", - pos="e,1392.3,193.6 2769.2,262.23 2407.5,258.4 1640.2,248.15 1520.4,229 1479.6,222.48 1434.8,208.57 1402,197.08", + lp="1556.9,221.5", + pos="e,1391.6,193.81 3519.2,264.04 3022.3,263.72 1710.8,259.91 1516.4,229 1476.6,222.68 1433.1,208.83 1401.2,197.3", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "gene to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1719.4,221.5", - pos="e,1533.6,191.69 2766.8,264.74 2461.7,264.91 1877.3,260.86 1672.4,229 1627.5,222.03 1577.9,206.88 1543.4,195.08", + lp="1712.4,221.5", + pos="e,1532.5,191.92 3519.3,263.73 3047,262.62 1845.1,257.04 1665.4,229 1622.5,222.31 1575.3,207.31 1542.3,195.48", style=solid]; predicate [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=2.1665]; "gene to phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="1873.4,221.5", - pos="e,1690.3,193.12 2767.7,263.18 2496.8,261.12 2012.7,253.96 1839.4,229 1791.5,222.1 1738.4,207.73 1700.2,196.15", + lp="1871.4,221.5", + pos="e,1689.4,193.16 3520.1,263.02 3077.5,260.37 2000.4,251.65 1837.4,229 1789.8,222.39 1737,207.91 1699.2,196.22", style=solid]; negated [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=1.2999]; "gene to phenotypic feature association" -> negated [color=blue, label=negated, - lp="2017.4,221.5", - pos="e,1825,190.33 2770.6,261.49 2532.5,257.55 2134.2,248.28 1988.4,229 1934.6,221.89 1874.4,205.41 1834.6,193.31", + lp="2013.4,221.5", + pos="e,1824.2,190.49 3520.8,262.44 3104.7,258.67 2133.2,247.95 1984.4,229 1931.8,222.3 1873.1,205.86 1834.2,193.65", style=solid]; qualifiers [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=2.1304]; "gene to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2149.9,221.5", - pos="e,1973.1,193.12 2771.5,261.08 2563,256.94 2237.9,247.71 2116.4,229 2070.6,221.94 2019.8,207.75 1983,196.28", + lp="2152.9,221.5", + pos="e,1973,193.12 3520.9,262.37 3129.6,258.61 2254.5,248.18 2119.4,229 2072.3,222.31 2020.1,207.84 1982.7,196.18", style=solid]; publications [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=1.7332]; "gene to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2287.4,221.5", - pos="e,2123.1,193.11 2773.1,260.46 2596,256.06 2341.1,246.84 2243.4,229 2205.1,222.01 2163.2,208.09 2132.6,196.71", + lp="2299.4,221.5", + pos="e,2124.2,192.77 3521.1,262.27 3156,258.49 2376.9,248.29 2255.4,229 2213.2,222.3 2166.8,207.8 2133.7,196.13", style=solid]; "has evidence" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=2.0943]; "gene to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2432.9,221.5", - pos="e,2278.6,194.09 2779.9,258.48 2640.8,253.15 2459,243.7 2386.4,229 2352.5,222.13 2315.7,208.99 2288,197.91", + lp="2459.9,221.5", + pos="e,2283,193.56 3518.7,264.94 3211.4,265.42 2620.3,261.82 2413.4,229 2371.7,222.39 2325.9,208.39 2292.5,196.89", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "gene to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2571.9,221.5", - pos="e,2461.7,196.09 2772.3,260.72 2670.2,256.74 2554.7,248.01 2507.4,229 2493.1,223.25 2479.6,212.88 2468.9,203.06", + lp="2616.9,221.5", + pos="e,2473.6,195.66 3520.6,262.5 3216.7,259.46 2643.6,250.88 2552.4,229 2528,223.14 2502.5,211.3 2482.6,200.62", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -143,8 +143,8 @@ digraph { width=3.015]; "gene to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2738.4,221.5", - pos="e,2656,195.74 2796.3,255.35 2724.9,249.83 2654.4,241.34 2643.4,229 2636,220.75 2640.5,211.17 2648.5,202.63", + lp="2790.4,221.5", + pos="e,2681.3,196.18 3519.7,263.18 3235.1,261.13 2727.2,253.98 2695.4,229 2688.4,223.47 2684.7,214.73 2682.8,206.08", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -153,8 +153,8 @@ digraph { width=3.015]; "gene to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2946.9,221.5", - pos="e,2864.2,193.89 2864.6,249.15 2855.2,244.15 2846.8,237.59 2840.4,229 2831.1,216.5 2840.2,206.22 2855,198.29", + lp="2999.9,221.5", + pos="e,2899.7,195.94 3520.7,262.41 3286.4,259.49 2914.8,251.34 2893.4,229 2886.8,222.07 2888.9,212.87 2893.9,204.26", style=solid]; timepoint [color=blue, height=0.5, @@ -163,8 +163,8 @@ digraph { width=1.5346]; "gene to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3105.4,221.5", - pos="e,3086.7,195.8 3016,247.8 3028.9,242.85 3042.1,236.64 3053.4,229 3063.5,222.2 3072.8,212.66 3080.3,203.73", + lp="3158.4,221.5", + pos="e,3102.3,196.37 3521.2,262.08 3362.6,258.93 3156.2,250.67 3123.4,229 3115.2,223.58 3109.6,214.62 3105.8,205.76", style=solid]; "original subject" [color=blue, height=0.5, @@ -173,8 +173,8 @@ digraph { width=1.0652]; "gene to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3222.4,221.5", - pos="e,3192.4,194.1 3074.1,250.77 3098,245.7 3122.5,238.69 3144.4,229 3153,225.2 3170,212.23 3184.6,200.45", + lp="3258.4,221.5", + pos="e,3201.4,195.9 3519.8,263.18 3385.1,260.56 3224.3,252.46 3202.4,229 3196.5,222.72 3196.3,213.94 3198.3,205.5", style=solid]; "original predicate" [color=blue, height=0.5, @@ -183,8 +183,8 @@ digraph { width=1.5887]; "gene to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3363.9,221.5", - pos="e,3314.6,195.9 3089.5,251.97 3175.2,243.79 3272.6,233.64 3281.4,229 3292.3,223.29 3301.6,213.59 3308.7,204.25", + lp="3387.9,221.5", + pos="e,3319.1,196.39 3531.3,258.57 3437.6,253.83 3339.1,245.06 3324.4,229 3318.9,222.96 3317.4,214.59 3317.8,206.43", style=solid]; "original object" [color=blue, height=0.5, @@ -193,162 +193,277 @@ digraph { width=1.0652]; "gene to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3491.9,221.5", - pos="e,3441,196.31 3091.8,252.22 3113.7,250.4 3136.2,248.6 3157.4,247 3187.8,244.71 3409,249.77 3431.4,229 3437.5,223.29 3440.1,214.88 \ -3440.8,206.57", + lp="3520.9,221.5", + pos="e,3444.6,196.15 3565.8,253.14 3524.7,247.85 3486.4,240.14 3469.4,229 3460.6,223.26 3453.9,214.11 3449,205.2", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3571.4,178", + width=2.1304]; + "gene to phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3643.9,221.5", + pos="e,3571.7,196.4 3614.7,249.24 3603.4,244.26 3592.9,237.68 3584.4,229 3578.5,222.97 3575.2,214.6 3573.3,206.44", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3742.4,178", + width=2.1304]; + "gene to phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3765.9,221.5", + pos="e,3722.6,195.74 3706.8,246.74 3706,236.82 3706.3,224.32 3710.4,214 3711.9,210.32 3713.9,206.79 3716.3,203.48", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3875.4,178", + width=1.0652]; + "gene to phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="3895.9,221.5", + pos="e,3861.7,194.97 3777.2,248.12 3792.3,243.16 3807.8,236.86 3821.4,229 3833.6,221.93 3845.3,211.65 3854.7,202.25", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3971.4,178", + width=1.0652]; + "gene to phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4014.4,221.5", + pos="e,3969.6,196.43 3864,254.45 3903.1,249.28 3938.3,241.3 3953.4,229 3960.4,223.3 3964.7,214.67 3967.3,206.17", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4104.4,178", + width=2.1304]; + "gene to phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4172.9,221.5", + pos="e,4096.7,196.39 3843.5,252.2 3943.4,243.21 4063.4,231.9 4068.4,229 4078,223.48 4085.7,214.25 4091.5,205.21", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4296.4,178", + width=2.1304]; + "gene to phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4363.9,221.5", + pos="e,4290.3,196.03 3842.2,252.07 3864.6,250.24 3887.7,248.47 3909.4,247 3948.8,244.33 4230.2,248.83 4264.4,229 4273.7,223.62 4280.7,\ +214.37 4285.7,205.28", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4486.4,178", + width=1.0652]; + "gene to phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4536.4,221.5", + pos="e,4479.4,196.14 3840.3,251.9 3863.3,250.05 3887,248.32 3909.4,247 3939.5,245.22 4424.9,243.35 4451.4,229 4461.2,223.7 4468.8,214.33 \ +4474.4,205.13", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4645.4,178", + width=1.0652]; + "gene to phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4689.4,221.5", + pos="e,4638,195.7 3839.5,251.82 3862.8,249.96 3886.8,248.25 3909.4,247 3948.2,244.85 4573.9,246.93 4608.4,229 4618.7,223.64 4626.9,213.95 \ +4632.9,204.52", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4796.4,178", + width=1.0652]; + "gene to phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4849.4,221.5", + pos="e,4788.4,195.75 3839,251.78 3862.4,249.91 3886.6,248.21 3909.4,247 3956.4,244.5 4715.3,250.12 4757.4,229 4768.1,223.64 4776.7,213.81 \ +4783.1,204.28", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4935.4,178", + width=1.0652]; + "gene to phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5005.9,221.5", + pos="e,4937.7,196.01 3838.4,251.75 3862,249.88 3886.4,248.18 3909.4,247 3937.6,245.55 4906,247.54 4927.4,229 4933.9,223.35 4936.6,214.68 \ +4937.5,206.15", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5076.4,178", + width=2.347]; + "gene to phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5155.9,221.5", + pos="e,5083.2,196.1 3838.1,251.73 3861.8,249.85 3886.3,248.16 3909.4,247 3941.9,245.37 5056.6,252.16 5079.4,229 5085.3,223.01 5086.3,\ +214.41 5085.3,206.03", style=solid]; type [height=0.5, - pos="3526.4,178", + pos="5210.4,178", width=0.86659]; "gene to phenotypic feature association" -> type [color=blue, label=type, - lp="3568.4,221.5", - pos="e,3540.7,194.16 3089.7,252.03 3112.3,250.19 3135.5,248.44 3157.4,247 3179,245.58 3532.4,244.69 3547.4,229 3554.4,221.67 3551.8,211.67 \ -3546.4,202.54", + lp="5250.4,221.5", + pos="e,5223.9,194.33 3838.1,251.7 3861.8,249.82 3886.3,248.14 3909.4,247 3927.7,246.1 5216.5,242.05 5229.4,229 5236.3,221.96 5234.2,212.12 \ +5229.4,203.04", style=solid]; category [height=0.5, - pos="3627.4,178", + pos="5311.4,178", width=1.4263]; "gene to phenotypic feature association" -> category [color=blue, label=category, - lp="3637.9,221.5", - pos="e,3619.1,196.15 3089.1,251.99 3111.9,250.15 3135.3,248.4 3157.4,247 3205.2,243.97 3545.8,250.92 3588.4,229 3598.8,223.66 3607.3,\ -214.16 3613.6,204.86", + lp="5321.9,221.5", + pos="e,5302.8,195.8 3837.9,251.71 3861.6,249.83 3886.2,248.14 3909.4,247 3947.2,245.15 5236.3,245.4 5270.4,229 5281.4,223.71 5290.4,213.89 \ +5297.2,204.35", style=solid]; subject [height=0.5, - pos="3741.4,178", + pos="5425.4,178", width=1.2277]; "gene to phenotypic feature association" -> subject [color=blue, label=subject, - lp="3728.4,221.5", - pos="e,3725.7,194.87 3088.6,251.91 3111.5,250.06 3135.1,248.33 3157.4,247 3214.7,243.57 3619.2,247.83 3673.4,229 3690,223.24 3705.9,211.93 \ -3718.2,201.51", + lp="5412.4,221.5", + pos="e,5409.8,195 3837.9,251.7 3861.6,249.81 3886.2,248.13 3909.4,247 3989.8,243.09 5281.1,254.55 5357.4,229 5374,223.43 5390,212.12 \ +5402.3,201.67", style=solid]; object [height=0.5, - pos="3784.4,91", + pos="5468.4,91", width=1.0832]; "gene to phenotypic feature association" -> object [color=blue, label=object, - lp="3827.4,178", - pos="e,3797.8,108.09 3087.8,251.88 3110.9,250.02 3134.9,248.29 3157.4,247 3224.1,243.17 3696.5,254.15 3758.4,229 3799.5,212.29 3802.2,\ -186.07 3807.4,142 3808.2,135.38 3809.3,133.39 3807.4,127 3806.4,123.55 3804.9,120.13 3803.1,116.85", + lp="5511.4,178", + pos="e,5481.8,108.09 3837.9,251.68 3861.6,249.8 3886.2,248.12 3909.4,247 3951.9,244.95 5402.8,244.67 5442.4,229 5483.7,212.67 5486.2,\ +186.07 5491.4,142 5492.2,135.38 5493.3,133.39 5491.4,127 5490.4,123.55 5488.9,120.13 5487.1,116.85", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3968.4,178", + pos="5652.4,178", width=2.3651]; "gene to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3956.4,221.5", - pos="e,3935.9,194.69 3087.5,251.84 3110.8,249.98 3134.8,248.26 3157.4,247 3307.9,238.61 3687.5,257.92 3835.4,229 3867,222.83 3900.9,209.98 \ -3926.5,198.85", + lp="5640.4,221.5", + pos="e,5620.2,194.72 3837.9,251.67 3861.6,249.79 3886.2,248.11 3909.4,247 3998.7,242.71 5431.5,245.49 5519.4,229 5551.1,223.05 5585.1,\ +210.13 5610.8,198.91", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4147.4,178", + pos="5831.4,178", width=2.1123]; "gene to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4137.4,221.5", - pos="e,4118.6,194.75 3087,251.77 3110.4,249.9 3134.6,248.2 3157.4,247 3254.1,241.9 3933.7,249.1 4028.4,229 4056.7,222.99 4086.8,210.31 \ -4109.6,199.22", + lp="5821.4,221.5", + pos="e,5802.6,194.85 3837.6,251.67 3861.4,249.78 3886.2,248.1 3909.4,247 4009.5,242.25 5614.3,249.28 5712.4,229 5740.7,223.14 5770.8,\ +210.46 5793.6,199.33", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4277.4,178", + pos="5961.4,178", width=1.011]; "gene to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4284.9,221.5", - pos="e,4260.7,194.26 3086.4,251.75 3110,249.87 3134.4,248.17 3157.4,247 3215.4,244.04 4147,246.3 4202.4,229 4220.8,223.25 4238.9,211.42 \ -4252.7,200.72", + lp="5969.9,221.5", + pos="e,5944.7,194.31 3837.6,251.65 3861.4,249.77 3886.2,248.09 3909.4,247 3964.3,244.42 5833.9,245.15 5886.4,229 5904.8,223.32 5922.9,\ +211.5 5936.7,200.78", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="4405.4,178", + pos="6089.4,178", width=2.0401]; "gene to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="4412.4,221.5", - pos="e,4389.8,195.71 3086.1,251.73 3109.8,249.85 3134.3,248.15 3157.4,247 3223,243.71 4278.3,250.64 4340.4,229 4356,223.55 4370.8,212.75 \ -4382.4,202.58", + lp="6097.4,221.5", + pos="e,6074.1,195.74 3837.3,251.66 3861.3,249.77 3886.1,248.09 3909.4,247 3968.1,244.26 5969.9,248.37 6025.4,229 6040.9,223.6 6055.5,\ +212.8 6066.8,202.62", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="4541.4,178", + pos="6225.4,178", width=1.2277]; "gene to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="4529.4,221.5", - pos="e,4522.8,194.54 3086.1,251.7 3109.8,249.83 3134.3,248.14 3157.4,247 3229.7,243.43 4390.9,249.24 4460.4,229 4480,223.28 4499.6,211.41 \ -4514.6,200.67", + lp="6213.4,221.5", + pos="e,6207.1,194.57 3837.3,251.66 3861.3,249.76 3886.1,248.08 3909.4,247 3971.4,244.12 6085.8,246.36 6145.4,229 6164.8,223.34 6184.2,\ +211.47 6199,200.72", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="4647.4,178", + pos="6331.4,178", width=1.2277]; "gene to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="4632.9,221.5", - pos="e,4629.4,194.54 3085.9,251.7 3109.6,249.82 3134.2,248.13 3157.4,247 3235.7,243.18 4493.2,251.31 4568.4,229 4587.6,223.29 4606.7,\ -211.42 4621.3,200.68", + lp="6316.9,221.5", + pos="e,6313.4,194.57 3837.3,251.65 3861.3,249.76 3886.1,248.08 3909.4,247 3974.4,243.99 6190,247.36 6252.4,229 6271.7,223.34 6290.8,211.47 \ +6305.3,200.72", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="4751.4,178", + pos="6435.4,178", width=1.1735]; "gene to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="4747.4,221.5", - pos="e,4732.7,194.31 3085.9,251.69 3109.6,249.81 3134.2,248.12 3157.4,247 3241.2,242.94 4587.6,251.96 4668.4,229 4688.5,223.27 4708.7,\ -211.28 4724.2,200.48", + lp="6431.4,221.5", + pos="e,6416.7,194.34 3837.3,251.64 3861.3,249.75 3886.1,248.08 3909.4,247 3977.2,243.87 6287.1,247.41 6352.4,229 6372.6,223.31 6392.8,\ +211.33 6408.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4858.4,178", + pos="6542.4,178", width=1.1735]; "gene to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="4877.4,221.5", - pos="e,4843.9,195.47 3085.6,251.69 3109.4,249.8 3134.2,248.11 3157.4,247 3202.9,244.82 4753.5,244.39 4796.4,229 4811.5,223.58 4825.6,\ -212.83 4836.6,202.67", + lp="6561.4,221.5", + pos="e,6528.4,195 3837.3,251.64 3861.3,249.75 3886.1,248.07 3909.4,247 3980.7,243.72 6413.1,253.01 6480.4,229 6495.7,223.54 6510,212.56 \ +6521,202.28", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3204.4,265", + pos="3956.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3335.4,265", + pos="4087.4,265", width=2.0762]; subject -> object [label=relation, - lp="3779.4,134.5", - pos="e,3766.5,107.23 3742.5,159.55 3743.7,149.57 3746.2,137.07 3751.4,127 3753.6,122.68 3756.5,118.52 3759.7,114.66"]; + lp="5463.4,134.5", + pos="e,5450.5,107.23 5426.5,159.55 5427.7,149.57 5430.2,137.07 5435.4,127 5437.6,122.68 5440.5,118.52 5443.7,114.66"]; relation [height=0.5, - pos="3729.4,18", + pos="5413.4,18", width=1.2999]; - subject -> relation [pos="e,3730.7,36.188 3740.1,159.79 3738,132.48 3734,78.994 3731.5,46.38", + subject -> relation [pos="e,5414.7,36.188 5424.1,159.79 5422,132.48 5418,78.994 5415.5,46.38", style=dotted]; "gene to phenotypic feature association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3538.4,265", + pos="4290.4,265", width=3.0692]; - object -> relation [pos="e,3742.2,35.54 3771.9,73.889 3765,64.939 3756.2,53.617 3748.4,43.584", + object -> relation [pos="e,5426.2,35.54 5455.9,73.889 5449,64.939 5440.2,53.617 5432.4,43.584", style=dotted]; "gene to phenotypic feature association_object" [color=blue, height=0.5, label="phenotypic feature", - pos="3765.4,265", + pos="4517.4,265", width=2.7442]; } diff --git a/graphviz/gene_to_phenotypic_feature_association.svg b/graphviz/gene_to_phenotypic_feature_association.svg index c169542dfa..e7d6771ed6 100644 --- a/graphviz/gene_to_phenotypic_feature_association.svg +++ b/graphviz/gene_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to phenotypic feature association - -gene to phenotypic feature association + +gene to phenotypic feature association @@ -24,7 +24,7 @@ gene to phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ gene to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,8 +50,8 @@ gene to phenotypic feature association->gene to entity association mixin - - + + uses @@ -63,9 +63,9 @@ gene to phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ gene to phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ gene to phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ gene to phenotypic feature association->description - - -description + + +description @@ -115,9 +115,9 @@ gene to phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ gene to phenotypic feature association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ gene to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ gene to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ gene to phenotypic feature association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ gene to phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ gene to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ gene to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ gene to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ gene to phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ gene to phenotypic feature association->original subject - - -original subject + + +original subject @@ -258,9 +258,9 @@ gene to phenotypic feature association->original predicate - - -original predicate + + +original predicate @@ -271,214 +271,357 @@ gene to phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +gene to phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +gene to phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +gene to phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +gene to phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +gene to phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +gene to phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +gene to phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +gene to phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +gene to phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +gene to phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +gene to phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + gene to phenotypic feature association->type - - -type + + +type - + category - -category + +category - + gene to phenotypic feature association->category - - -category + + +category - + subject - -subject + +subject - + gene to phenotypic feature association->subject - - -subject + + +subject - + object - -object + +object - + gene to phenotypic feature association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + gene to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + gene to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + gene to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier - + sex qualifier - -biological sex + +biological sex - + gene to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier - + has count - -integer + +integer - + gene to phenotypic feature association->has count - - -has count + + +has count - + has total - -integer + +integer - + gene to phenotypic feature association->has total - - -has total + + +has total - + has quotient - -double + +double - + gene to phenotypic feature association->has quotient - - -has quotient + + +has quotient - + has percentage - -double + +double - + gene to phenotypic feature association->has percentage - - -has percentage + + +has percentage - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to phenotypic feature association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene to phenotypic feature association_object - -phenotypic feature + +phenotypic feature diff --git a/graphviz/genomic_sequence_localization.gv b/graphviz/genomic_sequence_localization.gv index e698ec68c6..977d0a298c 100644 --- a/graphviz/genomic_sequence_localization.gv +++ b/graphviz/genomic_sequence_localization.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3868.1,283"]; + graph [bb="0,0,5599.1,283"]; node [label="\N"]; "genomic sequence localization" [height=0.5, label="genomic sequence localization", - pos="2175.5,265", + pos="2895.5,265", width=4.2066]; "sequence association" [height=0.5, pos="108.54,178", width=3.015]; "genomic sequence localization" -> "sequence association" [label=is_a, lp="372.54,221.5", - pos="e,165.68,193.45 2023.8,264.55 1647.6,265.37 679.36,263.89 358.54,229 295.84,222.18 225.48,207.46 175.41,195.75"]; + pos="e,165.17,193.42 2744.2,263.53 2233.8,261.73 594.74,254.03 358.54,229 295.61,222.33 225,207.52 174.91,195.73"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "genomic sequence localization" -> id [color=blue, label=id, lp="488.54,221.5", - pos="e,302.53,189.98 2024,264.41 1666.3,264.82 777.69,262.32 481.54,229 409.39,220.88 391.48,215.5 321.54,196 318.43,195.13 315.23,194.17 \ + pos="e,302.53,189.98 2744.3,263.47 2250.6,261.51 705.1,253.45 481.54,229 409.36,221.11 391.48,215.5 321.54,196 318.43,195.13 315.23,194.17 \ 312.04,193.15", style=solid]; iri [color=blue, @@ -30,8 +30,8 @@ digraph { "genomic sequence localization" -> iri [color=blue, label=iri, lp="601.54,221.5", - pos="e,407.45,190.2 2024.3,264.01 1684.2,263.49 867.56,259.04 593.54,229 518.77,220.8 500.36,214.85 427.54,196 424.16,195.13 420.69,194.16 \ -417.2,193.15", + pos="e,407.45,190.2 2744.6,263.29 2266.8,260.83 805.81,251.53 593.54,229 518.74,221.06 500.36,214.85 427.54,196 424.16,195.13 420.69,\ +194.16 417.2,193.15", style=solid]; name [color=blue, height=0.5, @@ -41,7 +41,7 @@ digraph { "genomic sequence localization" -> name [color=blue, label=name, lp="708.54,221.5", - pos="e,531.51,191.49 2023.8,264.79 1698.5,265.77 942.75,264.04 688.54,229 637.42,221.95 580.4,206.4 541.3,194.5", + pos="e,531.13,191.46 2744.3,263.66 2279.4,262.31 890.44,256.04 688.54,229 637.24,222.13 580.03,206.47 540.92,194.5", style=solid]; description [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { "genomic sequence localization" -> description [color=blue, label=description, lp="829.04,221.5", - pos="e,677.61,194.09 2025,262.8 1690.9,259.77 907.36,250.45 788.54,229 753.5,222.67 715.5,209.31 687.19,197.99", + pos="e,677.59,194.18 2743.9,264.24 2292.9,264.55 979.05,262.55 788.54,229 753.47,222.82 715.47,209.46 687.17,198.09", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genomic sequence localization" -> "has attribute" [color=blue, label="has attribute", - lp="975.54,221.5", - pos="e,818.36,192.76 2025.5,262.43 1717.5,258.83 1033.5,248.71 928.54,229 893.37,222.4 855.23,208.28 827.65,196.73", + lp="974.54,221.5", + pos="e,818.12,192.86 2744.1,264.15 2313.8,264.19 1103.9,261.37 927.54,229 892.57,222.58 854.7,208.45 827.34,196.84", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genomic sequence localization" -> negated [color=blue, label=negated, - lp="1132.5,221.5", - pos="e,940.11,190.37 2025.3,262.69 1773.6,259.9 1277,251.63 1103.5,229 1049.7,221.98 989.51,205.49 949.76,193.35", + lp="1129.5,221.5", + pos="e,939.56,190.5 2745,262.9 2342.6,259.68 1261.1,249.26 1100.5,229 1047.6,222.32 988.42,205.82 949.3,193.59", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genomic sequence localization" -> qualifiers [color=blue, label=qualifiers, - lp="1265,221.5", - pos="e,1088.2,193.18 2025.2,262.57 1798.5,259.72 1379.9,251.5 1231.5,229 1185.7,222.05 1134.9,207.84 1098.2,196.34", + lp="1269,221.5", + pos="e,1088.4,193.14 2745.1,262.87 2364.3,259.71 1382.3,249.66 1235.5,229 1188.2,222.33 1135.7,207.86 1098.1,196.19", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genomic sequence localization" -> publications [color=blue, label=publications, - lp="1402.5,221.5", - pos="e,1237.9,193.06 2025.5,262.39 1825.4,259.42 1482.2,251.18 1358.5,229 1320.1,222.11 1278.1,208.11 1247.5,196.67", + lp="1415.5,221.5", + pos="e,1239.6,192.78 2745,262.82 2386.9,259.68 1504.4,249.91 1371.5,229 1329.1,222.33 1282.4,207.82 1249.1,196.15", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "genomic sequence localization" -> "has evidence" [color=blue, label="has evidence", - lp="1548,221.5", - pos="e,1393.8,194.18 2027.1,261.24 1859.7,257.25 1598.4,248.15 1501.5,229 1467.6,222.29 1430.8,209.15 1403.1,198.02", + lp="1576,221.5", + pos="e,1398.4,193.58 2745.5,262.36 2415.5,258.43 1646.8,247.42 1529.5,229 1487.6,222.42 1441.6,208.42 1407.9,196.9", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "genomic sequence localization" -> "knowledge source" [color=blue, label="knowledge source", - lp="1687,221.5", - pos="e,1576.8,196.17 2023.9,264.76 1885.8,263.59 1693,256.72 1622.5,229 1608.2,223.35 1594.7,212.99 1584,203.16", + lp="1734,221.5", + pos="e,1588.8,195.42 2744.7,263.09 2440.1,260.77 1771.4,252.97 1669.5,229 1644.4,223.09 1618.1,211.05 1597.7,200.26", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "genomic sequence localization" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1853.5,221.5", - pos="e,1771.3,195.6 2027.5,261.21 1915.1,257.51 1776.9,248.92 1758.5,229 1751,220.79 1755.5,211.15 1763.7,202.54", + lp="1907.5,221.5", + pos="e,1797.2,196.25 2744.4,263.68 2455.2,262.44 1849,256.56 1812.5,229 1805.3,223.55 1801.3,214.82 1799.1,206.17", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "genomic sequence localization" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2063,221.5", - pos="e,1980.7,194.03 2041.1,256.71 2003,251.67 1968.7,243.21 1956.5,229 1946.2,216.84 1956,206.43 1971.6,198.31", + lp="2117,221.5", + pos="e,2015.8,196.05 2744.2,263.4 2498,261.67 2035.5,254.96 2010.5,229 2004.1,222.25 2005.8,213.2 2010.3,204.65", style=solid]; timepoint [color=blue, height=0.5, @@ -140,8 +140,8 @@ digraph { width=1.5346]; "genomic sequence localization" -> timepoint [color=blue, label=timepoint, - lp="2211.5,221.5", - pos="e,2191.5,194.53 2172.7,246.62 2171.8,236.66 2172,224.16 2176.5,214 2178.5,209.58 2181.3,205.46 2184.5,201.7", + lp="2275.5,221.5", + pos="e,2218,195.94 2744.4,263.64 2564.2,262.01 2282,255.24 2240.5,229 2232,223.57 2225.9,214.44 2221.8,205.45", style=solid]; "original subject" [color=blue, height=0.5, @@ -150,9 +150,8 @@ digraph { width=1.0652]; "genomic sequence localization" -> "original subject" [color=blue, label="original subject", - lp="2325.5,221.5", - pos="e,2303.4,192.7 2211.4,247.37 2222.8,241.81 2235.3,235.4 2246.5,229 2257.1,222.96 2259.3,220.57 2269.5,214 2277.7,208.79 2286.6,203.21 \ -2294.8,198.07", + lp="2375.5,221.5", + pos="e,2317.4,195.95 2749.9,260.08 2584.1,254.88 2334.2,244.53 2319.5,229 2313.7,222.84 2313.2,214.21 2314.7,205.84", style=solid]; "original predicate" [color=blue, height=0.5, @@ -161,8 +160,8 @@ digraph { width=1.5887]; "genomic sequence localization" -> "original predicate" [color=blue, label="original predicate", - lp="2465,221.5", - pos="e,2422.6,195.43 2298.1,254.34 2326.4,249.11 2355.8,241.13 2381.5,229 2389,225.48 2402.9,213.61 2415.2,202.31", + lp="2505,221.5", + pos="e,2435,196.05 2745.9,262.17 2621.9,259.09 2462.6,250.86 2441.5,229 2435.8,223.02 2434,214.53 2434.1,206.24", style=solid]; "original object" [color=blue, height=0.5, @@ -171,143 +170,258 @@ digraph { width=1.0652]; "genomic sequence localization" -> "original object" [color=blue, label="original object", - lp="2596,221.5", - pos="e,2550.6,196.2 2283.8,252.37 2301.4,250.54 2319.5,248.69 2336.5,247 2379.8,242.72 2496.2,254.43 2531.5,229 2539.3,223.44 2544.3,\ -214.57 2547.6,205.83", + lp="2639,221.5", + pos="e,2560.4,195.81 2752.2,259.11 2685.7,254.57 2615.4,245.83 2587.5,229 2578.1,223.3 2570.7,213.87 2565.2,204.72", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2686.5,178", + width=2.1304]; + "genomic sequence localization" -> "subject category" [color=blue, + label="subject category", + lp="2764,221.5", + pos="e,2688.4,196.31 2783,252.91 2749,247.55 2717.3,239.85 2704.5,229 2697.7,223.23 2693.5,214.69 2690.9,206.29", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2857.5,178", + width=2.1304]; + "genomic sequence localization" -> "object category" [color=blue, + label="object category", + lp="2885,221.5", + pos="e,2838.6,195.82 2849.1,247.74 2841.3,242.92 2834.2,236.78 2829.5,229 2824.7,220.9 2827.3,211.93 2832.5,203.84", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2990.5,178", + width=1.0652]; + "genomic sequence localization" -> "subject closure" [color=blue, + label="subject closure", + lp="3011,221.5", + pos="e,2975.7,194.83 2918.4,247.09 2925.6,241.51 2933.6,235.16 2940.5,229 2950.1,220.58 2960.1,210.78 2968.6,202.1", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3090.5,178", + width=1.0652]; + "genomic sequence localization" -> "object closure" [color=blue, + label="object closure", + lp="3131.5,221.5", + pos="e,3087.6,196.31 2997.8,251.64 3028.7,246.16 3057.7,238.71 3069.5,229 3076.7,223.17 3081.4,214.5 3084.6,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3223.5,178", + width=2.1304]; + "genomic sequence localization" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3290,221.5", + pos="e,3215.1,196.31 3001.8,252.14 3082.9,242.94 3181.4,231.36 3185.5,229 3195.4,223.33 3203.6,213.95 3209.8,204.83", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3415.5,178", + width=2.1304]; + "genomic sequence localization" -> "object category closure" [color=blue, + label="object category closure", + lp="3481,221.5", + pos="e,3408.8,196.04 3001.1,252.09 3019.6,250.23 3038.6,248.44 3056.5,247 3092.6,244.1 3350.1,246.8 3381.5,229 3391.1,223.58 3398.6,214.19 \ +3404,205", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3605.5,178", + width=1.0652]; + "genomic sequence localization" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3653.5,221.5", + pos="e,3598.1,195.67 2999.8,251.91 3018.7,250.03 3038.2,248.29 3056.5,247 3113.3,243.01 3518.2,255.51 3568.5,229 3578.8,223.59 3587,213.89 \ +3593,204.47", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3764.5,178", + width=1.0652]; + "genomic sequence localization" -> "object namespace" [color=blue, + label="object namespace", + lp="3807.5,221.5", + pos="e,3756.5,195.72 2999.4,251.83 3018.4,249.95 3038,248.22 3056.5,247 3093.6,244.55 3692.4,245.76 3725.5,229 3736.2,223.6 3744.9,213.77 \ +3751.3,204.25", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3915.5,178", + width=1.0652]; + "genomic sequence localization" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3967.5,221.5", + pos="e,3907.2,195.75 2998.9,251.8 3018.1,249.91 3037.9,248.19 3056.5,247 3102,244.11 3834.7,249.16 3875.5,229 3886.4,223.65 3895.2,213.82 \ +3901.8,204.29", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4086.5,178", + width=1.0652]; + "genomic sequence localization" -> "object label closure" [color=blue, + label="object label closure", + lp="4133,221.5", + pos="e,4077.9,195.78 2998.5,251.78 3017.8,249.88 3037.7,248.16 3056.5,247 3111.4,243.61 3996.1,252.96 4045.5,229 4056.5,223.68 4065.6,\ +213.86 4072.3,204.32", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4239.5,178", + width=2.347]; + "genomic sequence localization" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4292,221.5", + pos="e,4233.2,196.18 2998.5,251.74 3017.8,249.84 3037.7,248.14 3056.5,247 3088.4,245.07 4178.5,244.36 4206.5,229 4216.1,223.75 4223.4,\ +214.39 4228.6,205.19", style=solid]; type [height=0.5, - pos="2641.5,178", + pos="4373.5,178", width=0.86659]; "genomic sequence localization" -> type [color=blue, label=type, - lp="2673.5,221.5", - pos="e,2651.3,195.42 2281.6,252.07 2299.9,250.22 2318.8,248.45 2336.5,247 2371.5,244.16 2627.5,254.49 2651.5,229 2657.6,222.55 2657.4,\ -213.48 2654.9,204.83", + lp="4390.5,221.5", + pos="e,4375.9,196.02 2998.5,251.71 3017.8,249.82 3037.7,248.12 3056.5,247 3092.8,244.84 4338,252.78 4365.5,229 4372.1,223.36 4374.8,214.7 \ +4375.6,206.16", style=solid]; category [height=0.5, - pos="2742.5,178", + pos="4474.5,178", width=1.4263]; "genomic sequence localization" -> category [color=blue, label=category, - lp="2746,221.5", - pos="e,2731.4,195.7 2281.1,252.02 2299.6,250.16 2318.6,248.4 2336.5,247 2376.1,243.91 2657.3,245.3 2693.5,229 2705.8,223.47 2716.7,213.34 \ -2725,203.64", + lp="4470,221.5", + pos="e,4459.5,195.47 2998.1,251.75 3017.5,249.84 3037.6,248.12 3056.5,247 3131.6,242.55 4339.6,253.96 4410.5,229 4426.1,223.53 4440.8,\ +212.61 4452.2,202.37", style=solid]; "start interbase coordinate" [color=blue, height=0.5, label=integer, - pos="2856.5,178", + pos="4588.5,178", width=1.2277]; "genomic sequence localization" -> "start interbase coordinate" [color=blue, label="start interbase coordinate", - lp="2906,221.5", - pos="e,2839.2,194.61 2280.2,251.95 2299,250.08 2318.3,248.33 2336.5,247 2435.2,239.8 2687.4,259.59 2781.5,229 2799.7,223.11 2817.5,211.52 \ -2831.2,200.98", + lp="4633,221.5", + pos="e,4569.8,194.31 2998.1,251.74 3017.5,249.82 3037.6,248.12 3056.5,247 3136.9,242.27 4428.1,251.04 4505.5,229 4525.7,223.26 4545.9,\ +211.27 4561.3,200.47", style=solid]; "end interbase coordinate" [color=blue, height=0.5, label=integer, - pos="3030.5,178", + pos="4761.5,178", width=1.2277]; "genomic sequence localization" -> "end interbase coordinate" [color=blue, label="end interbase coordinate", - lp="3107,221.5", - pos="e,3026.2,196.04 2279.4,251.83 2298.4,249.95 2318,248.23 2336.5,247 2373.5,244.55 2972,248.42 3003.5,229 3012.2,223.69 3018.2,214.58 \ -3022.4,205.58", + lp="4835,221.5", + pos="e,4755.9,196.17 2998.1,251.71 3017.5,249.8 3037.6,248.1 3056.5,247 3103,244.31 4690,251.83 4730.5,229 4739.8,223.79 4746.6,214.57 \ +4751.5,205.46", style=solid]; "genome build" [color=blue, height=0.5, label=StrandEnum, - pos="3178.5,178", + pos="4909.5,178", width=1.9318]; "genomic sequence localization" -> "genome build" [color=blue, label="genome build", - lp="3254,221.5", - pos="e,3194.5,195.59 2278.9,251.78 2298.1,249.89 2317.9,248.18 2336.5,247 2360.5,245.49 3183.7,246.15 3200.5,229 3207.3,222.09 3205.2,\ -212.75 3200.2,204.01", + lp="4982,221.5", + pos="e,4924,195.74 2998.1,251.69 3017.5,249.78 3037.6,248.09 3056.5,247 3082.5,245.51 4910.2,247.47 4928.5,229 4935.1,222.34 4933.6,213.16 \ +4929.3,204.48", style=solid]; strand [color=blue, height=0.5, label=StrandEnum, - pos="3335.5,178", + pos="5066.5,178", width=1.9318]; "genomic sequence localization" -> strand [color=blue, label=strand, - lp="3345,221.5", - pos="e,3330.5,196.11 2278.5,251.79 2297.8,249.88 2317.7,248.16 2336.5,247 2363.4,245.33 3283.3,242.67 3306.5,229 3315.5,223.71 3322,214.48 \ -3326.5,205.38", + lp="5074,221.5", + pos="e,5060.6,196.19 2998.1,251.69 3017.5,249.78 3037.6,248.08 3056.5,247 3111.4,243.86 4986.5,255.6 5034.5,229 5044,223.76 5051.1,214.41 \ +5056.2,205.2", style=solid]; phase [color=blue, height=0.5, label=PhaseEnum, - pos="3488.5,178", + pos="5219.5,178", width=1.8234]; "genomic sequence localization" -> phase [color=blue, label=phase, - lp="3441,221.5", - pos="e,3461,194.54 2278.5,251.77 2297.8,249.87 2317.7,248.15 2336.5,247 2451.5,239.95 3260,253.24 3372.5,229 3400.3,223.02 3429.7,210.29 \ -3451.9,199.18", + lp="5170,221.5", + pos="e,5191.9,194.37 2998.1,251.68 3017.5,249.77 3037.6,248.08 3056.5,247 3170,240.53 4990.3,252.11 5101.5,229 5130.1,223.07 5160.3,210.13 \ +5183,198.89", style=solid]; subject [height=0.5, - pos="3616.5,178", + pos="5347.5,178", width=1.2277]; "genomic sequence localization" -> subject [color=blue, label=subject, - lp="3551.5,221.5", - pos="e,3587.3,191.71 2278.5,251.75 2297.8,249.85 2317.7,248.14 2336.5,247 2461.9,239.4 3342.8,250.1 3466.5,229 3505.4,222.37 3547.9,207.42 \ -3577.7,195.58", + lp="5281.5,221.5", + pos="e,5318.2,191.66 2998.1,251.67 3017.5,249.77 3037.6,248.08 3056.5,247 3175.2,240.25 5078.3,248.3 5195.5,229 5235.2,222.47 5278.7,\ +207.32 5308.9,195.4", style=solid]; object [height=0.5, - pos="3659.5,91", + pos="5390.5,91", width=1.0832]; "genomic sequence localization" -> object [color=blue, label=object, - lp="3710.5,178", - pos="e,3672.9,108.09 2278.5,251.73 2297.8,249.83 2317.7,248.13 2336.5,247 2474.6,238.73 3445.6,254.67 3581.5,229 3622.6,221.25 3641.9,\ -227.29 3669.5,196 3690.2,172.62 3691.5,156.9 3682.5,127 3681.5,123.55 3680,120.13 3678.3,116.85", + lp="5441.5,178", + pos="e,5403.9,108.09 2998.1,251.67 3017.5,249.76 3037.6,248.07 3056.5,247 3181.6,239.91 5188.3,251.62 5311.5,229 5353,221.38 5372.5,227.55 \ +5400.5,196 5421.3,172.66 5422.5,156.9 5413.5,127 5412.5,123.55 5411,120.13 5409.3,116.85", style=solid]; predicate [height=0.5, - pos="3813.5,178", + pos="5544.5,178", width=1.5165]; "genomic sequence localization" -> predicate [color=blue, label=predicate, - lp="3786.5,221.5", - pos="e,3789.7,194.33 2278.1,251.75 2297.5,249.83 2317.6,248.12 2336.5,247 2412.7,242.49 3636.3,246.59 3710.5,229 3735.4,223.11 3761.3,\ -210.51 3780.9,199.44", + lp="5517.5,221.5", + pos="e,5520.7,194.37 2997.6,251.7 3017.2,249.78 3037.5,248.08 3056.5,247 3188.8,239.53 5312.5,259.17 5441.5,229 5466.4,223.18 5492.3,\ +210.58 5511.9,199.49", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2383.5,265", + pos="3103.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2514.5,265", + pos="3234.5,265", width=2.0762]; subject -> object [label=relation, - lp="3654.5,134.5", - pos="e,3641.6,107.23 3617.6,159.55 3618.8,149.57 3621.3,137.07 3626.5,127 3628.8,122.68 3631.7,118.52 3634.9,114.66"]; + lp="5385.5,134.5", + pos="e,5372.6,107.23 5348.6,159.55 5349.8,149.57 5352.3,137.07 5357.5,127 5359.8,122.68 5362.7,118.52 5365.9,114.66"]; relation [height=0.5, - pos="3604.5,18", + pos="5335.5,18", width=1.2999]; - subject -> relation [pos="e,3605.8,36.188 3615.2,159.79 3613.2,132.48 3609.1,78.994 3606.6,46.38", + subject -> relation [pos="e,5336.8,36.188 5346.2,159.79 5344.2,132.48 5340.1,78.994 5337.6,46.38", style=dotted]; "genomic sequence localization_subject" [color=blue, height=0.5, label="nucleic acid entity", - pos="2702.5,265", + pos="3422.5,265", width=2.6539]; - object -> relation [pos="e,3617.4,35.54 3647.1,73.889 3640.1,64.939 3631.4,53.617 3623.6,43.584", + object -> relation [pos="e,5348.4,35.54 5378.1,73.889 5371.1,64.939 5362.4,53.617 5354.6,43.584", style=dotted]; "genomic sequence localization_object" [color=blue, height=0.5, label="nucleic acid entity", - pos="2911.5,265", + pos="3631.5,265", width=2.6539]; "genomic sequence localization_predicate" [color=blue, height=0.5, label="predicate type", - pos="3103.5,265", + pos="3823.5,265", width=2.1665]; } diff --git a/graphviz/genomic_sequence_localization.svg b/graphviz/genomic_sequence_localization.svg index 1ab6e5527b..1edc9a6b86 100644 --- a/graphviz/genomic_sequence_localization.svg +++ b/graphviz/genomic_sequence_localization.svg @@ -4,16 +4,16 @@ - + %3 - + genomic sequence localization - -genomic sequence localization + +genomic sequence localization @@ -24,8 +24,8 @@ genomic sequence localization->sequence association - - + + is_a @@ -37,7 +37,7 @@ genomic sequence localization->id - + id @@ -50,7 +50,7 @@ genomic sequence localization->iri - + iri @@ -63,8 +63,8 @@ genomic sequence localization->name - - + + name @@ -76,8 +76,8 @@ genomic sequence localization->description - - + + description @@ -89,9 +89,9 @@ genomic sequence localization->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genomic sequence localization->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genomic sequence localization->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genomic sequence localization->publications - - -publications + + +publications @@ -141,9 +141,9 @@ genomic sequence localization->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ genomic sequence localization->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ genomic sequence localization->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ genomic sequence localization->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ genomic sequence localization->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ genomic sequence localization->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ genomic sequence localization->original predicate - - -original predicate + + +original predicate @@ -232,194 +232,337 @@ genomic sequence localization->original object - - -original object + + +original object - + +subject category + +ontology class + + + +genomic sequence localization->subject category + + +subject category + + + +object category + +ontology class + + + +genomic sequence localization->object category + + +object category + + + +subject closure + +string + + + +genomic sequence localization->subject closure + + +subject closure + + + +object closure + +string + + + +genomic sequence localization->object closure + + +object closure + + + +subject category closure + +ontology class + + + +genomic sequence localization->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +genomic sequence localization->object category closure + + +object category closure + + + +subject namespace + +string + + + +genomic sequence localization->subject namespace + + +subject namespace + + + +object namespace + +string + + + +genomic sequence localization->object namespace + + +object namespace + + + +subject label closure + +string + + + +genomic sequence localization->subject label closure + + +subject label closure + + + +object label closure + +string + + + +genomic sequence localization->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +genomic sequence localization->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + genomic sequence localization->type - - -type + + +type - + category - -category + +category - + genomic sequence localization->category - - -category + + +category - + start interbase coordinate - -integer + +integer - + genomic sequence localization->start interbase coordinate - - -start interbase coordinate + + +start interbase coordinate - + end interbase coordinate - -integer + +integer - + genomic sequence localization->end interbase coordinate - - -end interbase coordinate + + +end interbase coordinate - + genome build - -StrandEnum + +StrandEnum - + genomic sequence localization->genome build - - -genome build + + +genome build - + strand - -StrandEnum + +StrandEnum - + genomic sequence localization->strand - - -strand + + +strand - + phase - -PhaseEnum + +PhaseEnum - + genomic sequence localization->phase - - -phase + + +phase - + subject - -subject + +subject - + genomic sequence localization->subject - - -subject + + +subject - + object - -object + +object - + genomic sequence localization->object - - -object + + +object - + predicate - -predicate + +predicate - + genomic sequence localization->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + genomic sequence localization_subject - -nucleic acid entity + +nucleic acid entity - + object->relation - - + + - + genomic sequence localization_object - -nucleic acid entity + +nucleic acid entity - + genomic sequence localization_predicate - -predicate type + +predicate type diff --git a/graphviz/genotype_as_a_model_of_disease_association.gv b/graphviz/genotype_as_a_model_of_disease_association.gv index 796f949243..7032d6fc59 100644 --- a/graphviz/genotype_as_a_model_of_disease_association.gv +++ b/graphviz/genotype_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4389.1,283"]; + graph [bb="0,0,6110.1,283"]; node [label="\N"]; "genotype as a model of disease association" [height=0.5, label="genotype as a model of disease association", - pos="2550.9,265", + pos="3443.9,265", width=5.8314]; "genotype to disease association" [height=0.5, pos="157.94,178", width=4.3871]; "genotype as a model of disease association" -> "genotype to disease association" [label=is_a, - lp="823.94,221.5", - pos="e,269.28,190.86 2342.1,263.03 2015.3,260.77 1362.8,253.35 809.94,229 594.09,219.49 540.22,214.28 324.94,196 310.17,194.75 294.68,\ -193.32 279.33,191.84"]; + lp="817.94,221.5", + pos="e,269.28,190.85 3235.6,262.74 2698.5,259.23 1275.8,248.37 803.94,229 590.72,220.25 537.56,214.14 324.94,196 310.17,194.74 294.68,\ +193.31 279.33,191.83"]; "model to disease association mixin" [height=0.5, pos="505.94,178", width=4.7843]; "genotype as a model of disease association" -> "model to disease association mixin" [label=uses, - lp="1045.4,221.5", - pos="e,615.95,191.85 2341.2,263.97 2047.5,262.83 1497.1,256.72 1028.9,229 890.45,220.8 731.91,204.69 626.03,192.97"]; + lp="1035.4,221.5", + pos="e,613.33,192.08 3234.7,263.21 2728.3,260.93 1447,252.91 1018.9,229 882.97,221.41 727.37,205.17 623.53,193.25"]; "entity to disease association mixin" [height=0.5, pos="866.94,178", width=4.7482]; "genotype as a model of disease association" -> "entity to disease association mixin" [label=uses, - lp="1192.4,221.5", - pos="e,942.76,194.2 2343.4,262.15 2016.4,258.65 1395.9,249.51 1175.9,229 1100.1,221.93 1014.6,207.61 952.85,196.1"]; + lp="1190.4,221.5", + pos="e,941.31,194.24 3233.8,264.68 2750.2,265.62 1569.7,264.09 1173.9,229 1098.1,222.28 1012.8,207.81 951.34,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "genotype as a model of disease association" -> id [color=blue, label=id, - lp="1312.9,221.5", - pos="e,1122.9,190.01 2343,262.45 2042.2,259.46 1500.4,251.13 1305.9,229 1232.1,220.59 1213.6,215.79 1141.9,196 1138.8,195.14 1135.6,194.18 \ -1132.4,193.17", + lp="1307.9,221.5", + pos="e,1122.9,189.98 3235.2,262.83 2733.8,259.69 1489.2,249.89 1300.9,229 1229.2,221.04 1211.4,215.43 1141.9,196 1138.8,195.13 1135.6,\ +194.17 1132.4,193.15", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "genotype as a model of disease association" -> iri [color=blue, label=iri, - lp="1430.9,221.5", - pos="e,1227.5,190.16 2345.1,261.45 2069.6,257.36 1595.5,247.83 1422.9,229 1344.3,220.41 1324.7,215.46 1247.9,196 1244.5,195.13 1241,194.16 \ -1237.4,193.14", + lp="1420.9,221.5", + pos="e,1227.8,190.19 3235.9,262.54 2754.3,258.86 1590.2,248.09 1412.9,229 1338.6,220.99 1320.3,214.78 1247.9,196 1244.6,195.12 1241.1,\ +194.16 1237.6,193.14", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "genotype as a model of disease association" -> name [color=blue, label=name, - lp="1535.9,221.5", - pos="e,1352.6,191.18 2343.7,261.99 2088.5,258.65 1670,250.07 1515.9,229 1462.5,221.7 1402.8,205.92 1362.2,194.03", + lp="1527.9,221.5", + pos="e,1351.7,191.54 3235.3,262.99 2769.9,260.33 1675.1,251.73 1507.9,229 1457.2,222.09 1400.6,206.58 1361.7,194.65", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "genotype as a model of disease association" -> description [color=blue, label=description, - lp="1655.4,221.5", - pos="e,1499.5,193.95 2342,263.03 2109.6,260.74 1749.2,253.24 1614.9,229 1578.4,222.41 1538.7,208.97 1509.1,197.69", + lp="1648.4,221.5", + pos="e,1497.7,194.15 3234.2,263.71 2786.3,262.56 1764,256.86 1607.9,229 1573.1,222.78 1535.4,209.42 1507.3,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "genotype as a model of disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1797.9,221.5", - pos="e,1639.5,192.73 2343.9,261.84 2145.3,258.52 1860.1,250.13 1750.9,229 1715.5,222.14 1676.9,208.11 1648.9,196.66", + lp="1793.9,221.5", + pos="e,1638.6,192.95 3234.6,263.5 2812.9,261.94 1889.3,255.5 1746.9,229 1712.5,222.58 1675.2,208.62 1648.1,197.07", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "genotype as a model of disease association" -> negated [color=blue, label=negated, - lp="1946.9,221.5", - pos="e,1760.2,190.33 2343.7,261.99 2219.6,258.44 2059.1,249.73 1917.9,229 1866.3,221.42 1808.6,205.31 1770,193.41", + lp="1948.9,221.5", + pos="e,1759.8,190.46 3233.9,264.63 2877.1,264.77 2167.4,260.86 1919.9,229 1867.4,222.23 1808.6,205.81 1769.7,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "genotype as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2077.4,221.5", - pos="e,1908.2,193.28 2350.2,259.67 2256.6,255.22 2144,246.4 2043.9,229 2000.7,221.48 1952.8,207.6 1917.7,196.37", + lp="2087.4,221.5", + pos="e,1908.7,193.2 3233.8,264.77 2902.9,264.96 2275,260.88 2053.9,229 2007.2,222.26 1955.5,207.87 1918.3,196.25", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "genotype as a model of disease association" -> publications [color=blue, label=publications, - lp="2210.9,221.5", - pos="e,2057.4,193.32 2366.4,256.39 2302.7,251.34 2231.2,242.94 2166.9,229 2132.4,221.52 2094.8,208.14 2066.8,197.11", + lp="2232.9,221.5", + pos="e,2059.7,192.85 3233.7,264.89 2930,265.03 2383.6,260.62 2188.9,229 2147.6,222.28 2102.1,207.95 2069.4,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.0943]; "genotype as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2350.4,221.5", - pos="e,2211.8,194.37 2417.4,251.1 2380.3,245.89 2340.2,238.73 2303.9,229 2275.6,221.39 2244.9,209.08 2221.2,198.58", + lp="2391.4,221.5", + pos="e,2217.9,193.63 3234.1,263.85 2964.1,262.53 2510,256.15 2344.9,229 2304.5,222.35 2260.2,208.52 2227.6,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=3.015]; "genotype as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2479.4,221.5", - pos="e,2389.3,196.24 2455.1,248.93 2440.9,244.04 2426.9,237.57 2414.9,229 2406.4,222.9 2399.5,213.84 2394.2,205.1", + lp="2546.4,221.5", + pos="e,2407.5,195.61 3238.6,261.16 2977.8,256.84 2552.9,247.12 2481.9,229 2458.8,223.1 2434.9,211.34 2416.2,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "genotype as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2646.9,221.5", - pos="e,2572.6,194.65 2547.1,246.59 2545.9,236.37 2546.1,223.63 2551.9,214 2555.1,208.82 2559.3,204.35 2564.1,200.52", + lp="2717.9,221.5", + pos="e,2613.9,196.33 3237.3,261.8 3001.5,258.31 2645.2,249.64 2622.9,229 2616.8,223.32 2614.4,214.91 2613.8,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -143,9 +143,8 @@ digraph { width=3.015]; "genotype as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2871.4,221.5", - pos="e,2808.3,194.64 2668.4,250.05 2693.2,245.02 2718.8,238.21 2741.9,229 2753.3,224.48 2754.1,219.64 2764.9,214 2775.7,208.42 2787.5,\ -203.13 2798.8,198.44", + lp="2926.4,221.5", + pos="e,2830.1,195.87 3244.4,259.34 3067.4,254.19 2834.6,244.52 2819.9,229 2812.8,221.43 2816.3,212.05 2823.1,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -154,8 +153,8 @@ digraph { width=1.5346]; "genotype as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3031.9,221.5", - pos="e,3018,195.38 2700.2,252.31 2822,242.69 2974.7,230.41 2977.9,229 2985.4,225.82 2998.7,214.01 3010.5,202.67", + lp="3080.9,221.5", + pos="e,3033.3,196.43 3254.5,257.2 3160.1,252.05 3062.6,243.34 3045.9,229 3039.4,223.36 3036.1,214.85 3034.5,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -164,9 +163,8 @@ digraph { width=1.0652]; "genotype as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3148.9,221.5", - pos="e,3124.8,193.27 2698.5,252.19 2722.3,250.38 2746.8,248.59 2769.9,247 2836.8,242.41 3007.4,250.32 3070.9,229 3072.3,228.55 3096,212.71 \ -3116.4,198.97", + lp="3178.9,221.5", + pos="e,3130.2,194.82 3270.2,254.87 3200.4,249.39 3133.8,241.08 3122.9,229 3116.3,221.56 3118.9,211.86 3124.3,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -175,9 +173,8 @@ digraph { width=1.5887]; "genotype as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3289.4,221.5", - pos="e,3244.6,195.46 2696.1,251.99 2720.7,250.16 2746,248.42 2769.9,247 2818.3,244.12 3161.2,247.62 3205.9,229 3213.2,225.96 3226.1,214.16 \ -3237.5,202.78", + lp="3305.4,221.5", + pos="e,3246.1,195.8 3298.7,251.97 3272.6,246.83 3250.8,239.48 3241.9,229 3236.1,222.05 3237.4,213.06 3241.2,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -186,121 +183,237 @@ digraph { width=1.0652]; "genotype as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3419.4,221.5", - pos="e,3372.6,196.31 2694.9,251.86 2719.9,250.03 2745.7,248.31 2769.9,247 2802.5,245.24 3329.6,248.14 3355.9,229 3363.3,223.62 3367.7,\ -214.91 3370.3,206.25", + lp="3429.4,221.5", + pos="e,3371.4,196.07 3397.9,247.43 3390.1,242.64 3382.9,236.59 3377.9,229 3373.5,222.32 3371.8,214 3371.3,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3506.9,178", + width=2.1304]; + "genotype as a model of disease association" -> "subject category" [color=blue, + label="subject category", + lp="3553.4,221.5", + pos="e,3501.5,196.22 3467.4,247.1 3473.6,241.81 3480,235.61 3484.9,229 3490.2,221.97 3494.5,213.49 3497.9,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3677.9,178", + width=2.1304]; + "genotype as a model of disease association" -> "object category" [color=blue, + label="object category", + lp="3696.4,221.5", + pos="e,3661.9,195.91 3555.9,249.66 3576.8,244.69 3598,238 3616.9,229 3630.5,222.54 3643.7,212.41 3654.3,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3810.9,178", + width=1.0652]; + "genotype as a model of disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3833.4,221.5", + pos="e,3797.9,195.42 3588,251.89 3662,244.94 3740,236.19 3755.9,229 3769.1,223.04 3781.3,212.72 3790.8,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3909.9,178", + width=1.0652]; + "genotype as a model of disease association" -> "object closure" [color=blue, + label="object closure", + lp="3953.9,221.5", + pos="e,3908.4,196.15 3593.7,252.36 3723.8,242.23 3891.7,229.14 3891.9,229 3899.2,223.45 3903.6,214.7 3906.1,206.05", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4042.9,178", + width=2.1304]; + "genotype as a model of disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4112.4,221.5", + pos="e,4035.9,196.07 3590.6,252.1 3614.7,250.29 3639.5,248.52 3662.9,247 3701.2,244.51 3974.4,247.61 4007.9,229 4017.7,223.61 4025.3,\ +214.23 4030.9,205.04", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4235.9,178", + width=2.1304]; + "genotype as a model of disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4303.4,221.5", + pos="e,4229.9,196.1 3588.2,251.89 3613.1,250.06 3638.8,248.34 3662.9,247 3693,245.34 4177.8,243.87 4203.9,229 4213.3,223.65 4220.4,214.27 \ +4225.5,205.08", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4425.9,178", + width=1.0652]; + "genotype as a model of disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4475.9,221.5", + pos="e,4418.9,196.18 3587,251.8 3612.3,249.96 3638.4,248.26 3662.9,247 3703.3,244.93 4355.3,248.13 4390.9,229 4400.7,223.74 4408.4,214.38 \ +4414,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4584.9,178", + width=1.0652]; + "genotype as a model of disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4628.9,221.5", + pos="e,4577.6,195.73 3586.4,251.75 3611.9,249.9 3638.2,248.21 3662.9,247 3712.1,244.6 4504.2,251.58 4547.9,229 4558.3,223.66 4566.4,213.98 \ +4572.5,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4735.9,178", + width=1.0652]; + "genotype as a model of disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4788.9,221.5", + pos="e,4727.9,195.76 3586.1,251.72 3611.7,249.86 3638.1,248.18 3662.9,247 3720.3,244.28 4645.5,254.65 4696.9,229 4707.6,223.66 4716.3,\ +213.83 4722.7,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4906.9,178", + width=1.0652]; + "genotype as a model of disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4954.4,221.5", + pos="e,4898.6,195.78 3585.5,251.71 3611.3,249.84 3637.9,248.16 3662.9,247 3696.3,245.45 4836.9,243.71 4866.9,229 4877.8,223.68 4886.6,\ +213.86 4893.2,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5048.9,178", + width=2.347]; + "genotype as a model of disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5110.4,221.5", + pos="e,5046.5,196.45 3585.5,251.67 3611.3,249.81 3637.9,248.14 3662.9,247 3700.8,245.28 4996.5,250.2 5027.9,229 5035.8,223.72 5040.7,\ +214.91 5043.8,206.14", style=solid]; type [height=0.5, - pos="3461.9,178", + pos="5182.9,178", width=0.86659]; "genotype as a model of disease association" -> type [color=blue, label=type, - lp="3495.9,221.5", - pos="e,3472.9,194.96 2694,251.82 2719.3,249.97 2745.4,248.27 2769.9,247 2789.5,245.99 3461.3,243.03 3474.9,229 3481.4,222.4 3480.5,213.03 \ -3477.2,204.19", + lp="5206.9,221.5", + pos="e,5188.9,196.12 3585.2,251.66 3611.1,249.8 3637.8,248.12 3662.9,247 3684,246.06 5169.1,244.03 5183.9,229 5189.8,223.03 5191.1,214.44 \ +5190.5,206.05", style=solid]; category [height=0.5, - pos="3562.9,178", + pos="5283.9,178", width=1.4263]; "genotype as a model of disease association" -> category [color=blue, label=category, - lp="3569.4,221.5", - pos="e,3552.5,195.81 2694,251.79 2719.3,249.95 2745.4,248.25 2769.9,247 2811.3,244.9 3478.1,245.91 3515.9,229 3528,223.61 3538.4,213.5 \ -3546.4,203.78", + lp="5283.4,221.5", + pos="e,5270.9,195.44 3585.2,251.66 3611.1,249.79 3637.8,248.12 3662.9,247 3706.3,245.07 5186.4,244.54 5226.9,229 5241,223.6 5254,212.99 \ +5263.9,202.93", style=solid]; predicate [height=0.5, - pos="3686.9,178", + pos="5407.9,178", width=1.5165]; "genotype as a model of disease association" -> predicate [color=blue, label=predicate, - lp="3672.9,221.5", - pos="e,3667.5,194.98 2693.7,251.76 2719.1,249.91 2745.3,248.22 2769.9,247 2862.6,242.41 3515.9,255.05 3604.9,229 3624.5,223.29 3644,211.66 \ -3659.1,201.05", + lp="5389.9,221.5", + pos="e,5387,194.81 3585.2,251.64 3611.1,249.78 3637.8,248.11 3662.9,247 3754.9,242.94 5230.1,252.77 5318.9,229 5340.2,223.32 5361.7,211.41 \ +5378.3,200.63", style=solid]; object [height=0.5, - pos="4273.9,91", + pos="5994.9,91", width=1.0832]; "genotype as a model of disease association" -> object [color=blue, label=object, - lp="3808.9,178", - pos="e,4235.2,94.237 2693.1,251.75 2718.7,249.89 2745.1,248.2 2769.9,247 2822.2,244.48 3661.9,247.15 3710.9,229 3732.6,221 3733.9,211.5 \ -3750.9,196 3767.7,180.78 3766.7,170.09 3786.9,160 3863.3,121.97 4117.2,101.88 4224.9,94.891", + lp="5529.9,178", + pos="e,5956.2,94.237 3584.9,251.65 3610.9,249.78 3637.7,248.11 3662.9,247 3711.9,244.85 5381.5,244.74 5427.9,229 5451.1,221.15 5453.5,\ +212.02 5471.9,196 5489,181.17 5487.7,170.09 5507.9,160 5584.3,121.97 5838.2,101.88 5945.9,94.891", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3924.9,178", + pos="5645.9,178", width=2.3651]; "genotype as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3912.9,221.5", - pos="e,3892.5,194.78 2693.1,251.72 2718.7,249.87 2745.1,248.18 2769.9,247 2883.4,241.6 3680.4,250.29 3791.9,229 3823.5,222.97 3857.4,\ -210.12 3883.1,198.96", + lp="5633.9,221.5", + pos="e,5613.8,194.73 3584.9,251.64 3610.9,249.77 3637.7,248.1 3662.9,247 3765.6,242.52 5411.9,247.87 5512.9,229 5544.7,223.08 5578.7,\ +210.15 5604.4,198.93", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4103.9,178", + pos="5824.9,178", width=2.1123]; "genotype as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4093.9,221.5", - pos="e,4075.1,194.8 2692.5,251.7 2718.3,249.84 2744.9,248.16 2769.9,247 2904.8,240.77 3852.8,256.66 3984.9,229 4013.3,223.07 4043.3,210.39 \ -4066.1,199.28", + lp="5814.9,221.5", + pos="e,5796.1,194.86 3584.9,251.62 3610.9,249.75 3637.7,248.09 3662.9,247 3776.3,242.1 5594.8,251.92 5705.9,229 5734.3,223.15 5764.3,\ +210.47 5787.1,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4233.9,178", + pos="5954.9,178", width=1.011]; "genotype as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4241.4,221.5", - pos="e,4217.3,194.29 2692.5,251.67 2718.3,249.81 2744.9,248.13 2769.9,247 2847,243.51 4085.2,251.84 4158.9,229 4177.4,223.28 4195.5,211.46 \ -4209.3,200.75", + lp="5962.4,221.5", + pos="e,5938.3,194.31 3584.6,251.63 3610.6,249.75 3637.6,248.08 3662.9,247 3724.5,244.37 5821.1,247.09 5879.9,229 5898.4,223.33 5916.5,\ +211.51 5930.3,200.79", style=solid]; subject [height=0.5, - pos="4344.9,178", + pos="6065.9,178", width=1.2277]; "genotype as a model of disease association" -> subject [color=blue, label=subject, - lp="4343.9,221.5", - pos="e,4334.2,195.87 2692.2,251.66 2718.1,249.8 2744.8,248.12 2769.9,247 2812.3,245.11 4258,245.86 4296.9,229 4309.2,223.69 4319.8,213.6 \ -4328,203.86", + lp="6064.9,221.5", + pos="e,6055.2,195.89 3584.6,251.62 3610.6,249.74 3637.6,248.08 3662.9,247 3728.3,244.22 5957.9,254.88 6017.9,229 6030.2,223.72 6040.8,\ +213.63 6049,203.88", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2816.9,265", + pos="3709.9,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2947.9,265", + pos="3840.9,265", width=2.0762]; "genotype to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3118.9,265", + pos="4011.9,265", width=2.1665]; relation [height=0.5, - pos="4308.9,18", + pos="6029.9,18", width=1.2999]; - object -> relation [pos="e,4300.5,36.198 4282.2,73.174 4286.3,64.896 4291.3,54.723 4295.9,45.438", + object -> relation [pos="e,6021.5,36.198 6003.2,73.174 6007.3,64.896 6012.3,54.723 6016.9,45.438", style=dotted]; "genotype to disease association_object" [color=blue, height=0.5, label="named thing", - pos="3284.9,265", + pos="4177.9,265", width=1.9318]; subject -> object [label=relation, - lp="4302.9,134.5", - pos="e,4270.1,109.01 4308.6,167.42 4295.7,162.12 4282.6,154.06 4274.9,142 4270.7,135.26 4269.3,126.93 4269.4,119.01"]; - subject -> relation [pos="e,4313.1,36.005 4341.3,160.05 4336.8,139.44 4329,103.63 4321.9,73 4319.9,64.183 4317.6,54.574 4315.5,45.938", + lp="6023.9,134.5", + pos="e,5991.1,109.01 6029.6,167.42 6016.7,162.12 6003.6,154.06 5995.9,142 5991.7,135.26 5990.3,126.93 5990.4,119.01"]; + subject -> relation [pos="e,6034.1,36.005 6062.3,160.05 6057.8,139.44 6050,103.63 6042.9,73 6040.9,64.183 6038.6,54.574 6036.5,45.938", style=dotted]; "genotype as a model of disease association_subject" [color=blue, height=0.5, label=genotype, - pos="3425.9,265", + pos="4318.9,265", width=1.4985]; } diff --git a/graphviz/genotype_as_a_model_of_disease_association.svg b/graphviz/genotype_as_a_model_of_disease_association.svg index 5354d68e7b..7153942da0 100644 --- a/graphviz/genotype_as_a_model_of_disease_association.svg +++ b/graphviz/genotype_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype as a model of disease association - -genotype as a model of disease association + +genotype as a model of disease association @@ -24,9 +24,9 @@ genotype as a model of disease association->genotype to disease association - - -is_a + + +is_a @@ -37,9 +37,9 @@ genotype as a model of disease association->model to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ genotype as a model of disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ genotype as a model of disease association->id - - -id + + +id @@ -76,9 +76,9 @@ genotype as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ genotype as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ genotype as a model of disease association->description - - -description + + +description @@ -115,9 +115,9 @@ genotype as a model of disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ genotype as a model of disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ genotype as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ genotype as a model of disease association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ genotype as a model of disease association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ genotype as a model of disease association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ genotype as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ genotype as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ genotype as a model of disease association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ genotype as a model of disease association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ genotype as a model of disease association->original predicate - - -original predicate + + +original predicate @@ -258,168 +258,311 @@ genotype as a model of disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +genotype as a model of disease association->subject category + + +subject category + + + +object category + +ontology class + + + +genotype as a model of disease association->object category + + +object category + + + +subject closure + +string + + + +genotype as a model of disease association->subject closure + + +subject closure + + + +object closure + +string + + + +genotype as a model of disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +genotype as a model of disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +genotype as a model of disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +genotype as a model of disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +genotype as a model of disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +genotype as a model of disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +genotype as a model of disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +genotype as a model of disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + genotype as a model of disease association->type - - -type + + +type - + category - -category + +category - + genotype as a model of disease association->category - - -category + + +category - + predicate - -predicate + +predicate - + genotype as a model of disease association->predicate - - -predicate + + +predicate - + object - -object + +object - + genotype as a model of disease association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + genotype as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + genotype as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + genotype as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + subject - -subject + +subject - + genotype as a model of disease association->subject - - -subject + + +subject - + association_type - -string + +string - + association_category - -category type + +category type - + genotype to disease association_predicate - -predicate type + +predicate type - + relation - -relation + +relation - + object->relation - - + + - + genotype to disease association_object - -named thing + +named thing - + subject->object - - -relation + + +relation - + subject->relation - - + + - + genotype as a model of disease association_subject - -genotype + +genotype diff --git a/graphviz/genotype_to_disease_association.gv b/graphviz/genotype_to_disease_association.gv index 107303c058..77a41a4b55 100644 --- a/graphviz/genotype_to_disease_association.gv +++ b/graphviz/genotype_to_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4225.4,283"]; + graph [bb="0,0,5946.4,283"]; node [label="\N"]; "genotype to disease association" [height=0.5, label="genotype to disease association", - pos="2374.4,265", + pos="3267.4,265", width=4.3871]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to disease association" -> association [label=is_a, - lp="645.39,221.5", - pos="e,106.72,190.68 2216.9,263.27 1911.1,261.32 1215.7,254.25 631.39,229 410.23,219.44 353.31,228.88 134.39,196 128.62,195.13 122.62,\ -194.04 116.66,192.82"]; + lp="638.39,221.5", + pos="e,106.72,190.67 3110.1,263.03 2618.1,259.84 1112.7,248.66 624.39,229 406.3,220.22 350.23,228.52 134.39,196 128.62,195.13 122.62,\ +194.03 116.66,192.81"]; "genotype to entity association mixin" [height=0.5, pos="322.39,178", width=4.9829]; "genotype to disease association" -> "genotype to entity association mixin" [label=uses, - lp="868.89,221.5", - pos="e,435.43,192.01 2216.5,264.06 1939.9,263.34 1349.8,258.14 852.39,229 712.74,220.82 552.94,204.83 445.64,193.13"]; + lp="858.89,221.5", + pos="e,432.51,192.21 3110.1,263.41 2645.7,261.38 1285.9,253.48 842.39,229 704.99,221.42 547.8,205.26 442.54,193.35"]; "entity to disease association mixin" [height=0.5, pos="690.39,178", width=4.7482]; "genotype to disease association" -> "entity to disease association mixin" [label=uses, - lp="1015.9,221.5", - pos="e,766.22,194.2 2217.8,262.67 1909,259.62 1231.4,250.63 999.39,229 923.54,221.93 838.09,207.61 776.31,196.1"]; + lp="1013.9,221.5", + pos="e,764.77,194.24 3109.4,264.57 2664.8,265.69 1408.3,265.43 997.39,229 921.6,222.28 836.24,207.81 774.8,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "genotype to disease association" -> id [color=blue, label=id, - lp="1136.4,221.5", - pos="e,946.37,190.01 2217.4,262.92 1931.3,260.4 1335.4,252.45 1129.4,229 1055.5,220.59 1037.1,215.79 965.39,196 962.28,195.14 959.08,\ -194.18 955.89,193.17", + lp="1131.4,221.5", + pos="e,946.38,189.98 3110.1,263.14 2648.8,260.39 1319.5,250.64 1124.4,229 1052.7,221.04 1034.9,215.43 965.39,196 962.29,195.13 959.09,\ +194.17 955.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "genotype to disease association" -> iri [color=blue, label=iri, - lp="1254.4,221.5", - pos="e,1051,190.16 2218.2,262.15 1954.1,258.53 1429.8,249.02 1246.4,229 1167.7,220.41 1148.1,215.46 1071.4,196 1068,195.13 1064.4,194.16 \ -1060.9,193.14", + lp="1244.4,221.5", + pos="e,1051.3,190.19 3110.5,262.93 2666.3,259.65 1420.3,248.81 1236.4,229 1162,220.99 1143.8,214.78 1071.4,196 1068,195.12 1064.5,194.16 \ +1061.1,193.14", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "genotype to disease association" -> name [color=blue, label=name, - lp="1359.4,221.5", - pos="e,1176,191.18 2217.7,262.62 1971.3,259.78 1504.2,251.54 1339.4,229 1286,221.7 1226.2,205.92 1185.6,194.03", + lp="1351.4,221.5", + pos="e,1175.2,191.54 3110.1,263.27 2680,260.98 1505,252.61 1331.4,229 1280.6,222.09 1224,206.58 1185.1,194.65", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "genotype to disease association" -> description [color=blue, label=description, - lp="1478.9,221.5", - pos="e,1323,193.95 2216.8,263.47 1990,261.79 1583,255.1 1438.4,229 1401.9,222.41 1362.1,208.97 1332.6,197.69", + lp="1471.9,221.5", + pos="e,1321.2,194.15 3109.6,263.83 2694.7,262.98 1593.9,258 1431.4,229 1396.6,222.78 1358.8,209.42 1330.7,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "genotype to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1621.4,221.5", - pos="e,1463,192.73 2217.7,262.61 2020.5,259.9 1693.2,251.99 1574.4,229 1538.9,222.14 1500.4,208.11 1472.4,196.66", + lp="1617.4,221.5", + pos="e,1462,192.95 3109.9,263.68 2717.8,262.46 1718.9,256.65 1570.4,229 1535.9,222.58 1498.6,208.62 1471.5,197.07", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "genotype to disease association" -> negated [color=blue, label=negated, - lp="1770.4,221.5", - pos="e,1583.6,190.33 2217.2,263.2 2088.6,260.65 1902.4,252.65 1741.4,229 1689.8,221.42 1632,205.31 1593.5,193.41", + lp="1772.4,221.5", + pos="e,1583.2,190.46 3109.4,264.57 2774.8,265.1 2003.6,262.49 1743.4,229 1690.8,222.23 1632.1,205.81 1593.2,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "genotype to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1900.9,221.5", - pos="e,1731.7,193.28 2219.2,261.57 2118.3,257.95 1984.3,249.32 1867.4,229 1824.1,221.48 1776.2,207.6 1741.2,196.37", + lp="1910.9,221.5", + pos="e,1732.1,193.2 3109.4,264.7 2797.1,265.33 2110.7,262.65 1877.4,229 1830.7,222.26 1778.9,207.87 1741.7,196.25", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "genotype to disease association" -> publications [color=blue, label=publications, - lp="2034.4,221.5", - pos="e,1880.8,193.32 2225.4,258.94 2153.7,254.34 2066.9,245.61 1990.4,229 1955.9,221.52 1918.3,208.14 1890.3,197.11", + lp="2056.4,221.5", + pos="e,1883.1,192.85 3109.5,264.82 2820.8,265.46 2218.8,262.53 2012.4,229 1971,222.28 1925.6,207.95 1892.8,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.0943]; "genotype to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2173.9,221.5", - pos="e,2035.3,194.37 2255.7,253.11 2214.7,247.78 2168.6,240.05 2127.4,229 2099,221.39 2068.4,209.08 2044.7,198.58", + lp="2214.9,221.5", + pos="e,2041.4,193.63 3109.6,264.06 2850.1,263.3 2344.6,257.98 2168.4,229 2128,222.35 2083.6,208.52 2051.1,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=3.015]; "genotype to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2302.9,221.5", - pos="e,2212.8,196.24 2282.5,250.22 2266.9,245.2 2251.5,238.34 2238.4,229 2229.8,222.9 2222.9,213.84 2217.6,205.1", + lp="2369.9,221.5", + pos="e,2230.9,195.61 3111.7,261.95 2859.2,258.09 2381.1,248.32 2305.4,229 2282.3,223.1 2258.3,211.34 2239.6,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "genotype to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2470.4,221.5", - pos="e,2396,194.65 2370.6,246.59 2369.3,236.37 2369.5,223.63 2375.4,214 2378.6,208.82 2382.8,204.35 2387.6,200.52", + lp="2541.4,221.5", + pos="e,2437.4,196.33 3110.6,262.49 2879,259.52 2470.3,251.16 2446.4,229 2440.3,223.32 2437.9,214.91 2437.3,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -143,9 +143,8 @@ digraph { width=3.015]; "genotype to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2694.9,221.5", - pos="e,2631.7,194.64 2482.6,251.86 2510.2,246.69 2539.4,239.37 2565.4,229 2576.7,224.48 2577.6,219.64 2588.4,214 2599.1,208.42 2610.9,\ -203.13 2622.3,198.44", + lp="2749.9,221.5", + pos="e,2653.6,195.87 3113.9,260.61 2934.4,255.88 2659.4,245.91 2643.4,229 2636.2,221.43 2639.7,212.05 2646.6,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -154,9 +153,8 @@ digraph { width=1.5346]; "genotype to disease association" -> timepoint [color=blue, label=timepoint, - lp="2857.4,221.5", - pos="e,2841.4,195.4 2485.7,252.16 2504.3,250.33 2523.4,248.54 2541.4,247 2599.1,242.07 2748,251.5 2801.4,229 2808.8,225.86 2822.2,214.06 \ -2834,202.7", + lp="2904.4,221.5", + pos="e,2856.8,196.43 3117.7,259.19 3012.9,254.42 2888.4,245.38 2869.4,229 2862.9,223.36 2859.5,214.85 2858,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -165,9 +163,8 @@ digraph { width=1.0652]; "genotype to disease association" -> "original subject" [color=blue, label="original subject", - lp="2972.4,221.5", - pos="e,2948.3,193.27 2484.4,252.01 2503.4,250.16 2522.9,248.41 2541.4,247 2619.7,241.02 2819.8,253.67 2894.4,229 2895.7,228.56 2919.4,\ -212.71 2939.8,198.98", + lp="3002.4,221.5", + pos="e,2953.6,194.82 3124.9,257.13 3045,251.78 2958.8,242.88 2946.4,229 2939.7,221.56 2942.3,211.86 2947.8,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -176,9 +173,8 @@ digraph { width=1.5887]; "genotype to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3112.9,221.5", - pos="e,3068.1,195.47 2483,251.92 2502.4,250.05 2522.5,248.31 2541.4,247 2595.5,243.25 2979.2,249.72 3029.4,229 3036.7,225.98 3049.6,214.17 \ -3060.9,202.79", + lp="3128.9,221.5", + pos="e,3069.6,195.8 3137.6,254.69 3104.8,249.53 3075.9,241.49 3065.4,229 3059.5,222.05 3060.9,213.06 3064.7,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -187,121 +183,238 @@ digraph { width=1.0652]; "genotype to disease association" -> "original object" [color=blue, label="original object", - lp="3242.9,221.5", - pos="e,3196,196.32 2482.5,251.82 2502.1,249.95 2522.3,248.24 2541.4,247 2576.8,244.7 3150.7,249.8 3179.4,229 3186.8,223.63 3191.2,214.92 \ -3193.8,206.26", + lp="3252.9,221.5", + pos="e,3194.9,196.07 3221.7,247.64 3213.8,242.81 3206.5,236.69 3201.4,229 3197,222.32 3195.2,214 3194.8,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3330.4,178", + width=2.1304]; + "genotype to disease association" -> "subject category" [color=blue, + label="subject category", + lp="3376.9,221.5", + pos="e,3325,196.22 3290.8,247.1 3297.1,241.81 3303.5,235.61 3308.4,229 3313.6,221.97 3317.9,213.49 3321.3,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3501.4,178", + width=2.1304]; + "genotype to disease association" -> "object category" [color=blue, + label="object category", + lp="3519.9,221.5", + pos="e,3485.3,195.91 3371.6,251.43 3394.9,246.31 3419.1,239.12 3440.4,229 3454,222.54 3467.2,212.41 3477.8,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3634.4,178", + width=1.0652]; + "genotype to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3656.9,221.5", + pos="e,3621.3,195.42 3379.4,252.24 3467,242.92 3574.7,231.12 3579.4,229 3592.6,223.04 3604.7,212.72 3614.3,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3733.4,178", + width=1.0652]; + "genotype to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3777.4,221.5", + pos="e,3731.9,196.2 3378.3,252.12 3397,250.29 3416.2,248.5 3434.4,247 3465.6,244.42 3690.4,247.8 3715.4,229 3722.7,223.5 3727.1,214.76 \ +3729.6,206.11", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3866.4,178", + width=2.1304]; + "genotype to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3935.9,221.5", + pos="e,3859.4,196.09 3376.9,251.96 3396.1,250.11 3415.8,248.37 3434.4,247 3478.4,243.76 3792.7,250.27 3831.4,229 3841.1,223.64 3848.8,\ +214.27 3854.4,205.07", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4059.4,178", + width=2.1304]; + "genotype to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4126.9,221.5", + pos="e,4053.4,196.11 3375.5,251.86 3395.1,249.98 3415.3,248.26 3434.4,247 3467.3,244.83 3998.7,245.26 4027.4,229 4036.8,223.66 4043.9,\ +214.29 4049,205.09", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4249.4,178", + width=1.0652]; + "genotype to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4299.4,221.5", + pos="e,4242.4,196.18 3375.1,251.78 3394.8,249.91 3415.2,248.2 3434.4,247 3477.7,244.3 4176.2,249.46 4214.4,229 4224.2,223.75 4231.9,214.39 \ +4237.5,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4408.4,178", + width=1.0652]; + "genotype to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4452.4,221.5", + pos="e,4401,195.73 3374.6,251.77 3394.5,249.88 3415,248.17 3434.4,247 3486.4,243.86 4325.1,252.88 4371.4,229 4381.7,223.67 4389.9,213.99 \ +4395.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4559.4,178", + width=1.0652]; + "genotype to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4612.4,221.5", + pos="e,4551.4,195.77 3374.6,251.72 3394.5,249.84 3415,248.14 3434.4,247 3494.6,243.44 4466.4,255.92 4520.4,229 4531.1,223.66 4539.8,213.84 \ +4546.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4730.4,178", + width=1.0652]; + "genotype to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4777.9,221.5", + pos="e,4722.1,195.79 3374.2,251.73 3394.2,249.83 3414.9,248.13 3434.4,247 3469.2,244.98 4659.1,244.34 4690.4,229 4701.2,223.69 4710.1,\ +213.87 4716.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4872.4,178", + width=2.347]; + "genotype to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4933.9,221.5", + pos="e,4870,196.45 3374.2,251.71 3394.2,249.81 3414.9,248.11 3434.4,247 3473.7,244.75 4818.7,251 4851.4,229 4859.2,223.72 4864.1,214.91 \ +4867.2,206.14", style=solid]; type [height=0.5, - pos="3285.4,178", + pos="5006.4,178", width=0.86659]; "genotype to disease association" -> type [color=blue, label=type, - lp="3319.4,221.5", - pos="e,3296.4,194.96 2482.1,251.8 2501.8,249.92 2522.2,248.2 2541.4,247 2562.4,245.68 3283.7,244.05 3298.4,229 3304.8,222.4 3304,213.04 \ -3300.7,204.2", + lp="5030.4,221.5", + pos="e,5012.3,196.12 3374.2,251.69 3394.2,249.79 3414.9,248.1 3434.4,247 3456.2,245.77 4992,244.54 5007.4,229 5013.3,223.03 5014.6,214.44 \ +5013.9,206.05", style=solid]; category [height=0.5, - pos="3386.4,178", + pos="5107.4,178", width=1.4263]; "genotype to disease association" -> category [color=blue, label=category, - lp="3392.9,221.5", - pos="e,3375.9,195.82 2482.1,251.78 2501.8,249.9 2522.2,248.19 2541.4,247 2585.7,244.25 3298.9,247.06 3339.4,229 3351.5,223.62 3361.9,\ -213.51 3369.9,203.78", + lp="5106.9,221.5", + pos="e,5094.4,195.45 3374.2,251.68 3394.2,249.79 3414.9,248.1 3434.4,247 3479.2,244.47 5008.5,245.05 5050.4,229 5064.5,223.6 5077.4,212.99 \ +5087.4,202.94", style=solid]; subject [height=0.5, - pos="3500.4,178", + pos="5221.4,178", width=1.2277]; "genotype to disease association" -> subject [color=blue, label=subject, - lp="3484.4,221.5", - pos="e,3483.9,194.72 2481.6,251.78 2501.5,249.89 2522.1,248.18 2541.4,247 2590.6,244 3381.5,244.21 3428.4,229 3445.9,223.34 3462.8,211.92 \ -3475.9,201.42", + lp="5201.4,221.5", + pos="e,5203.4,194.55 3374.2,251.67 3394.2,249.78 3414.9,248.09 3434.4,247 3529.1,241.69 5051.4,255.9 5142.4,229 5161.7,223.31 5180.7,\ +211.44 5195.3,200.69", style=solid]; predicate [height=0.5, - pos="3617.4,178", + pos="5338.4,178", width=1.5165]; "genotype to disease association" -> predicate [color=blue, label=predicate, - lp="3590.4,221.5", - pos="e,3593.5,194.29 2481.6,251.75 2501.5,249.87 2522,248.16 2541.4,247 2649.3,240.52 3409.2,254.2 3514.4,229 3539.3,223.04 3565.1,210.45 \ -3584.7,199.39", + lp="5308.4,221.5", + pos="e,5314,194.11 3374.2,251.66 3394.2,249.77 3414.9,248.09 3434.4,247 3534.1,241.44 5134,251.14 5231.4,229 5257.4,223.09 5284.6,210.27 \ +5305.1,199.1", style=solid]; object [height=0.5, - pos="3567.4,91", + pos="5288.4,91", width=1.0832]; "genotype to disease association" -> object [color=blue, label=object, - lp="3709.4,178", - pos="e,3599.5,101.28 2481.6,251.72 2501.5,249.84 2522,248.14 2541.4,247 2601.7,243.44 3570.5,246.08 3628.4,229 3665.5,218.06 3700.5,193.63 \ -3681.4,160 3666,132.81 3634.9,115.34 3609,104.93", + lp="5430.4,178", + pos="e,5318.2,102.71 3374.2,251.65 3394.2,249.76 3414.9,248.08 3434.4,247 3540.5,241.11 5244,257.43 5346.4,229 5374.2,221.27 5388.1,221.08 \ +5402.4,196 5424.7,156.94 5368.7,124.38 5327.5,106.59", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3855.4,178", + pos="5576.4,178", width=2.3651]; "genotype to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3843.4,221.5", - pos="e,3823.2,194.68 2481.6,251.7 2501.5,249.82 2522,248.13 2541.4,247 2672.4,239.35 3593.5,253.45 3722.4,229 3754.1,222.99 3788.1,210.07 \ -3813.8,198.87", + lp="5564.4,221.5", + pos="e,5544.2,194.74 3373.7,251.69 3393.9,249.78 3414.8,248.09 3434.4,247 3545.8,240.84 5333.7,249.45 5443.4,229 5475.1,223.09 5509.1,\ +210.17 5534.8,198.94", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4034.4,178", + pos="5755.4,178", width=2.1123]; "genotype to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4024.4,221.5", - pos="e,4005.6,194.82 2481.2,251.71 2501.2,249.81 2521.9,248.12 2541.4,247 2693.8,238.26 3765.9,260.15 3915.4,229 3943.7,223.09 3973.8,\ -210.41 3996.6,199.3", + lp="5745.4,221.5", + pos="e,5726.6,194.86 3373.7,251.68 3393.9,249.77 3414.8,248.08 3434.4,247 3556.5,240.3 5516.6,253.66 5636.4,229 5664.8,223.16 5694.8,\ +210.48 5717.6,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4171.4,178", + pos="5892.4,178", width=1.011]; "genotype to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4173.9,221.5", - pos="e,4153.5,193.83 2481.2,251.69 2501.2,249.79 2521.9,248.1 2541.4,247 2627.3,242.14 4006.7,252.73 4089.4,229 4109.6,223.19 4129.8,\ -210.96 4145.1,200.04", + lp="5894.9,221.5", + pos="e,5874.5,193.85 3373.7,251.67 3393.9,249.76 3414.8,248.07 3434.4,247 3500.3,243.4 5746.9,247.09 5810.4,229 5830.6,223.23 5850.9,\ +211 5866.1,200.07", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2588.4,265", + pos="3481.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2719.4,265", + pos="3612.4,265", width=2.0762]; subject -> object [label=relation, - lp="3566.4,134.5", - pos="e,3554.7,108.05 3513.3,160.61 3523.3,147.95 3537.3,130.24 3548.5,115.98"]; + lp="5287.4,134.5", + pos="e,5275.7,108.05 5234.3,160.61 5244.3,147.95 5258.3,130.24 5269.5,115.98"]; relation [height=0.5, - pos="3512.4,18", + pos="5233.4,18", width=1.2999]; - subject -> relation [pos="e,3511.1,36.188 3501.7,159.79 3503.8,132.48 3507.8,78.994 3510.3,46.38", + subject -> relation [pos="e,5232.1,36.188 5222.7,159.79 5224.8,132.48 5228.8,78.994 5231.3,46.38", style=dotted]; "genotype to disease association_subject" [color=blue, height=0.5, label="named thing", - pos="2881.4,265", + pos="3774.4,265", width=1.9318]; "genotype to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3047.4,265", + pos="3940.4,265", width=2.1665]; - object -> relation [pos="e,3525.2,35.54 3554.9,73.889 3548,64.939 3539.2,53.617 3531.4,43.584", + object -> relation [pos="e,5246.2,35.54 5275.9,73.889 5269,64.939 5260.2,53.617 5252.4,43.584", style=dotted]; "genotype to disease association_object" [color=blue, height=0.5, label="named thing", - pos="3213.4,265", + pos="4106.4,265", width=1.9318]; } diff --git a/graphviz/genotype_to_disease_association.svg b/graphviz/genotype_to_disease_association.svg index 2dbfe50e32..1600312660 100644 --- a/graphviz/genotype_to_disease_association.svg +++ b/graphviz/genotype_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to disease association - -genotype to disease association + +genotype to disease association @@ -24,9 +24,9 @@ genotype to disease association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ genotype to disease association->genotype to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ genotype to disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ genotype to disease association->id - - -id + + +id @@ -76,9 +76,9 @@ genotype to disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ genotype to disease association->name - - -name + + +name @@ -102,9 +102,9 @@ genotype to disease association->description - - -description + + +description @@ -115,9 +115,9 @@ genotype to disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ genotype to disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ genotype to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ genotype to disease association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ genotype to disease association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ genotype to disease association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ genotype to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ genotype to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ genotype to disease association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ genotype to disease association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ genotype to disease association->original predicate - - -original predicate + + +original predicate @@ -258,168 +258,311 @@ genotype to disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +genotype to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +genotype to disease association->object category + + +object category + + + +subject closure + +string + + + +genotype to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +genotype to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +genotype to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +genotype to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +genotype to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +genotype to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +genotype to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +genotype to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +genotype to disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + genotype to disease association->type - - -type + + +type - + category - -category + +category - + genotype to disease association->category - - -category + + +category - + subject - -subject + +subject - + genotype to disease association->subject - - -subject + + +subject - + predicate - -predicate + +predicate - + genotype to disease association->predicate - - -predicate + + +predicate - + object - -object + +object - + genotype to disease association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + genotype to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + genotype to disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + genotype to disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + genotype to disease association_subject - -named thing + +named thing - + genotype to disease association_predicate - -predicate type + +predicate type - + object->relation - - + + - + genotype to disease association_object - -named thing + +named thing diff --git a/graphviz/genotype_to_gene_association.gv b/graphviz/genotype_to_gene_association.gv index 608e76626f..8304b56dcf 100644 --- a/graphviz/genotype_to_gene_association.gv +++ b/graphviz/genotype_to_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3006.4,283"]; + graph [bb="0,0,4738.4,283"]; node [label="\N"]; "genotype to gene association" [height=0.5, label="genotype to gene association", - pos="1551.4,265", + pos="2468.4,265", width=4.0441]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to gene association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1405.9,263.89 1117.9,263.03 484.15,257.8 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2323.2,263.58 1865.2,262 468.8,255.08 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "genotype to gene association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1406.9,262.67 1141.4,259.72 585.35,251.05 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2323.3,263.12 1882.8,260.25 579.73,250.04 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "genotype to gene association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1407.9,261.86 1164.5,257.79 680.64,247.61 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2323.7,262.92 1899.9,259.54 680.48,248.24 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "genotype to gene association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1407.4,262.23 1181.6,258.85 754.2,249.86 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2323.3,263.22 1913.4,260.75 765.25,251.86 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "genotype to gene association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1406.6,262.93 1200.3,260.57 832.32,253.02 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2322.9,263.73 1927.8,262.62 854.12,257.03 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genotype to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1407.7,261.9 1231.3,258.45 942.64,249.77 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2323,263.57 1950.1,262.07 979.07,255.64 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genotype to gene association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1408.1,261.64 1297.4,258.18 1140.5,249.7 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2322.9,264.31 2005.6,264.38 1260,260.99 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genotype to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1412.9,259.43 1329.8,254.98 1222.4,246.23 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2322.9,264.36 2027.9,264.39 1368.8,260.76 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genotype to gene association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1425.4,255.97 1370.8,250.81 1306.4,242.44 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2322.9,264.33 2051.6,264.18 1478.5,260.04 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "genotype to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1465.1,250.47 1437.1,245.04 1406.1,237.92 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2323.1,263.68 2079.9,262.37 1600.9,256.28 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "genotype to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1506.9,247.82 1498.1,242.92 1489.7,236.72 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2325.3,261.67 2090.5,257.35 1642.2,246.89 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "genotype to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.4,247.25 1591.3,241.57 1602.4,235.12 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2324.5,261.97 2111.5,258.31 1734.8,249.03 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "genotype to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1653.2,252.07 1727.7,243.17 1817.1,232.05 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,\ -202.83 1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2328.4,259.97 2167.5,254.65 1923.6,244.13 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "genotype to gene association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.19 1652.6,252.03 1670.5,250.17 1689,248.39 1706.4,247 1785.1,240.69 1987.8,257.76 2061.4,229 2069.3,225.89 2084,213.75 \ -2096.8,202.21", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2337.6,257.08 2251.6,251.37 2152.2,242.06 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "genotype to gene association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1652.2,251.92 1670.2,250.06 1688.8,248.31 1706.4,247 1805.8,239.56 2059.5,259.3 2154.4,229 2166,225.29 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2327,260.54 2277.4,256.1 2230.1,247.04 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "genotype to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.5 1651.3,251.87 1669.6,249.99 1688.6,248.25 1706.4,247 1771,242.46 2229,252.51 2289.4,229 2297.1,225.99 2311.2,213.99 \ -2323.5,202.5", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2383.3,250.35 2361,244.96 2341.3,237.9 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "genotype to gene association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.43 1650.9,251.82 1669.3,249.93 1688.4,248.2 1706.4,247 1747,244.28 2405.6,251.68 2439.4,229 2447.3,223.71 2452.4,214.89 \ -2455.6,206.12", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "genotype to gene association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2538.8,249.24 2551,244.31 2562.8,237.74 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "genotype to gene association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2568.4,251.91 2627.6,244.29 2693.5,234.83 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "genotype to gene association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.57 2571.7,252.25 2589,250.41 2606.7,248.59 2623.4,247 2672.7,242.3 2800.2,249.12 2845.4,229 2858.3,223.24 2870.1,212.94 \ +2879.3,203.18", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "genotype to gene association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2997,196.24 2569.6,252.03 2587.5,250.16 2606,248.39 2623.4,247 2663,243.83 2948.5,252.65 2980.4,229 2987.7,223.55 2992.1,214.82 \ +2994.7,206.17", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "genotype to gene association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.12 2568.8,251.94 2586.9,250.05 2605.7,248.3 2623.4,247 2675.8,243.13 3050.2,254.17 3096.4,229 3106.2,223.68 3113.8,\ +214.31 3119.4,205.11", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "genotype to gene association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.11 2567.9,251.86 2586.3,249.96 2605.4,248.22 2623.4,247 2660.5,244.47 3260.2,247.52 3292.4,229 3301.6,223.71 3308.4,\ +214.48 3313.3,205.38", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "genotype to gene association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.19 2567.5,251.81 2586.1,249.91 2605.3,248.18 2623.4,247 2670.8,243.91 3436.5,251.38 3478.4,229 3488.2,223.76 3495.9,\ +214.41 3501.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "genotype to gene association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.74 2567.5,251.77 2586.1,249.86 2605.3,248.15 2623.4,247 2679.5,243.43 3585.4,254.75 3635.4,229 3645.7,223.68 3653.9,214 \ +3659.9,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "genotype to gene association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.77 2567.5,251.73 2586,249.83 2605.3,248.13 2623.4,247 2655.6,244.99 3755.5,243.37 3784.4,229 3795.1,223.67 3803.8,213.84 \ +3810.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "genotype to gene association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2567.1,251.75 2585.8,249.83 2605.2,248.12 2623.4,247 2660.3,244.73 3921.2,245.24 3954.4,229 3965.3,223.69 3974.1,\ +213.87 3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "genotype to gene association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2567.1,251.72 2585.8,249.81 2605.2,248.11 2623.4,247 2664.8,244.49 4079.2,249.12 4115.4,229 4124.9,223.75 4131.9,\ +214.39 4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "genotype to gene association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.3,195.51 1650.9,251.77 1669.3,249.88 1688.4,248.17 1706.4,247 1730,245.46 2542.8,245.93 2559.4,229 2565.6,222.66 2565.4,213.61 \ -2562.9,204.96", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2567.1,251.71 2585.8,249.8 2605.2,248.1 2623.4,247 2646.3,245.62 4257.2,244.14 4274.4,229 4280.9,223.32 4283.4,214.65 \ +4284.1,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "genotype to gene association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.84 1650.5,251.8 1669.1,249.9 1688.3,248.17 1706.4,247 1756,243.79 2555.7,248.72 2601.4,229 2613.8,223.65 2624.6,213.55 \ -2632.9,203.82", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2567.1,251.7 2585.8,249.79 2605.2,248.09 2623.4,247 2670.4,244.18 4275,244.74 4319.4,229 4334.6,223.59 4349,212.84 \ +4360.1,202.68", style=solid]; predicate [height=0.5, - pos="2774.4,178", + pos="4506.4,178", width=1.5165]; "genotype to gene association" -> predicate [color=blue, label=predicate, - lp="2759.4,221.5", - pos="e,2754.4,195 1650.5,251.77 1669.1,249.87 1688.3,248.16 1706.4,247 1815.5,240.03 2585.2,258.97 2690.4,229 2710.3,223.32 2730.3,211.7 \ -2745.8,201.08", + lp="4485.4,221.5", + pos="e,4484.7,194.58 2567.1,251.69 2585.8,249.79 2605.2,248.09 2623.4,247 2722.7,241.07 4317.1,253.77 4413.4,229 4435.8,223.25 4458.7,\ +211.04 4476.1,200.13", style=solid]; subject [height=0.5, - pos="2891.4,178", + pos="4623.4,178", width=1.2277]; "genotype to gene association" -> subject [color=blue, label=subject, - lp="2861.4,221.5", - pos="e,2870.2,194.05 1650.5,251.75 1669,249.85 1688.3,248.14 1706.4,247 1827.4,239.38 2680,259.31 2797.4,229 2820.3,223.1 2843.7,210.64 \ -2861.5,199.63", + lp="4590.4,221.5", + pos="e,4601.1,193.87 2567.1,251.69 2585.8,249.78 2605.2,248.08 2623.4,247 2728.8,240.74 4420.8,253.74 4523.4,229 4547.9,223.1 4573.2,\ +210.33 4592.3,199.18", style=solid]; object [height=0.5, - pos="2934.4,91", + pos="4666.4,91", width=1.0832]; "genotype to gene association" -> object [color=blue, label=object, - lp="2984.4,178", - pos="e,2947.8,108.09 1650.5,251.73 1669,249.83 1688.3,248.13 1706.4,247 1772.1,242.91 2828.2,247.58 2891.4,229 2918,221.17 2928.2,218.5 \ -2944.4,196 2962.7,170.69 2966.3,156.9 2957.4,127 2956.4,123.55 2954.9,120.13 2953.1,116.85", + lp="4716.4,178", + pos="e,4679.8,108.09 2567.1,251.68 2585.8,249.77 2605.2,248.08 2623.4,247 2734.1,240.44 4513.5,258.67 4620.4,229 4648.2,221.27 4659.2,\ +219.22 4676.4,196 4695,170.92 4698.3,156.9 4689.4,127 4688.4,123.55 4686.9,120.13 4685.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1753.4,265", + pos="2670.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1884.4,265", + pos="2801.4,265", width=2.0762]; "genotype to gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2055.4,265", + pos="2972.4,265", width=2.1665]; subject -> object [label=relation, - lp="2929.4,134.5", - pos="e,2916.5,107.23 2892.5,159.55 2893.7,149.57 2896.2,137.07 2901.4,127 2903.6,122.68 2906.5,118.52 2909.7,114.66"]; + lp="4661.4,134.5", + pos="e,4648.5,107.23 4624.5,159.55 4625.7,149.57 4628.2,137.07 4633.4,127 4635.6,122.68 4638.5,118.52 4641.7,114.66"]; relation [height=0.5, - pos="2879.4,18", + pos="4611.4,18", width=1.2999]; - subject -> relation [pos="e,2880.7,36.188 2890.1,159.79 2888,132.48 2884,78.994 2881.5,46.38", + subject -> relation [pos="e,4612.7,36.188 4622.1,159.79 4620,132.48 4616,78.994 4613.5,46.38", style=dotted]; "genotype to gene association_subject" [color=blue, height=0.5, label=genotype, - pos="2205.4,265", + pos="3122.4,265", width=1.4985]; - object -> relation [pos="e,2892.2,35.54 2921.9,73.889 2915,64.939 2906.2,53.617 2898.4,43.584", + object -> relation [pos="e,4624.2,35.54 4653.9,73.889 4647,64.939 4638.2,53.617 4630.4,43.584", style=dotted]; "genotype to gene association_object" [color=blue, height=0.5, label=gene, - pos="2310.4,265", + pos="3227.4,265", width=0.92075]; } diff --git a/graphviz/genotype_to_gene_association.svg b/graphviz/genotype_to_gene_association.svg index 67bd9b1d61..5d2ae880df 100644 --- a/graphviz/genotype_to_gene_association.svg +++ b/graphviz/genotype_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to gene association - -genotype to gene association + +genotype to gene association @@ -24,9 +24,9 @@ genotype to gene association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ genotype to gene association->id - - -id + + +id @@ -50,9 +50,9 @@ genotype to gene association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ genotype to gene association->name - - -name + + +name @@ -76,9 +76,9 @@ genotype to gene association->description - - -description + + +description @@ -89,9 +89,9 @@ genotype to gene association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genotype to gene association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genotype to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genotype to gene association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ genotype to gene association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ genotype to gene association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ genotype to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ genotype to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ genotype to gene association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ genotype to gene association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ genotype to gene association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ genotype to gene association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +genotype to gene association->subject category + + +subject category + + + +object category + +ontology class + + + +genotype to gene association->object category + + +object category + + + +subject closure + +string + + + +genotype to gene association->subject closure + + +subject closure + + + +object closure + +string + + + +genotype to gene association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +genotype to gene association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +genotype to gene association->object category closure + + +object category closure + + + +subject namespace + +string + + + +genotype to gene association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +genotype to gene association->object namespace + + +object namespace + + + +subject label closure + +string + + + +genotype to gene association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +genotype to gene association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +genotype to gene association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + genotype to gene association->type - - -type + + +type - + category - -category + +category - + genotype to gene association->category - - -category + + +category - + predicate - -predicate + +predicate - + genotype to gene association->predicate - - -predicate + + +predicate - + subject - -subject + +subject - + genotype to gene association->subject - - -subject + + +subject - + object - -object + +object - + genotype to gene association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + genotype to gene association_predicate - -predicate type + +predicate type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + genotype to gene association_subject - -genotype + +genotype - + object->relation - - + + - + genotype to gene association_object - -gene + +gene diff --git a/graphviz/genotype_to_genotype_part_association.gv b/graphviz/genotype_to_genotype_part_association.gv index b449f644f9..19182ff911 100644 --- a/graphviz/genotype_to_genotype_part_association.gv +++ b/graphviz/genotype_to_genotype_part_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3006.4,283"]; + graph [bb="0,0,4738.4,283"]; node [label="\N"]; "genotype to genotype part association" [height=0.5, label="genotype to genotype part association", - pos="1551.4,265", + pos="2468.4,265", width=5.2356]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to genotype part association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1363.4,263.74 1059.6,262.49 474.08,256.45 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2280.6,263.43 1784.4,261.58 462.87,254.31 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "genotype to genotype part association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1365.2,262.19 1087,258.82 575.79,249.96 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,194.18 \ -219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2280.9,262.84 1804.8,259.62 573.95,249.41 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "genotype to genotype part association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1367.2,261.16 1114.1,256.68 671.67,246.62 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2281.4,262.57 1824.3,258.82 674.85,247.63 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "genotype to genotype part association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1366.1,261.58 1132.8,257.76 745.43,248.65 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2281.1,262.96 1839.9,260.16 759.77,251.12 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "genotype to genotype part association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1364.7,262.4 1153.8,259.53 823.88,251.47 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2280.4,263.6 1856.1,262.21 848.77,256.08 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genotype to genotype part association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1367.4,261.06 1190.2,257.12 934.95,248.26 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2280.3,263.38 1881.1,261.58 973.89,254.68 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genotype to genotype part association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1369.5,260.29 1262.6,256.14 1125.3,247.39 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2279.7,264.3 1942.5,264.03 1249.3,259.61 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genotype to genotype part association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1379.8,257.5 1302.5,252.6 1210.4,244.02 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2279.8,264.34 1968,263.99 1358.4,259.29 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genotype to genotype part association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1403.5,253.78 1354.1,248.53 1299,240.69 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2279.8,264.27 1995,263.69 1468.6,258.48 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "genotype to genotype part association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1458.8,249.24 1432.5,243.98 1404.1,237.26 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2280.5,263.41 2027.7,261.63 1591.7,254.76 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "genotype to genotype part association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1506.2,247.43 1497.7,242.58 1489.5,236.51 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2284.7,260.9 2042.3,256.18 1638.3,245.9 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "genotype to genotype part association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.7,247.07 1591.6,241.44 1602.5,235.06 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2284,261.24 2067,257.14 1733.4,247.81 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "genotype to genotype part association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1686.4,252.43 1742.1,246.48 1799.6,238.48 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,\ -202.83 1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2291.5,258.71 2132.7,253.07 1922.6,243.01 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "genotype to genotype part association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.18 1683.4,252.15 1705.4,250.32 1728.1,248.53 1749.4,247 1818.7,242.03 1996.8,254.51 2061.4,229 2069.3,225.86 2084,213.72 \ -2096.8,202.19", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2310.3,255.17 2231.7,249.38 2150.5,240.7 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "genotype to genotype part association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1682.1,252.01 1704.5,250.17 1727.6,248.42 1749.4,247 1839.3,241.15 2068.6,256.58 2154.4,229 2166,225.26 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2297.8,257.28 2259.8,252.11 2227,243.43 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "genotype to genotype part association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.49 1681,251.89 1703.8,250.04 1727.3,248.32 1749.4,247 1809.3,243.43 2233.5,250.84 2289.4,229 2297.1,225.98 2311.2,213.98 \ -2323.5,202.49", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2378.3,249.11 2358.1,243.89 2340.8,237.23 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,205 @@ digraph { width=1.0652]; "genotype to genotype part association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.43 1680.2,251.82 1703.2,249.96 1727,248.25 1749.4,247 1787.7,244.86 2407.6,250.37 2439.4,229 2447.3,223.7 2452.4,214.88 \ -2455.6,206.11", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "genotype to genotype part association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2541,248.35 2552.4,243.53 2563.4,237.23 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "genotype to genotype part association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2621.2,254.37 2650.3,249 2679.9,240.96 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "genotype to genotype part association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.51 2603.8,252.46 2709.6,243.27 2839.7,231.55 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "genotype to genotype part association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2997,196.22 2600.4,252.14 2622.4,250.31 2645.1,248.53 2666.4,247 2701.3,244.51 2952.4,249.9 2980.4,229 2987.7,223.53 2992.1,214.79 \ +2994.7,206.14", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "genotype to genotype part association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.11 2598.8,251.99 2621.3,250.14 2644.5,248.4 2666.4,247 2714.1,243.95 3054.5,251.97 3096.4,229 3106.2,223.66 3113.8,\ +214.29 3119.4,205.09", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "genotype to genotype part association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.1 2597.5,251.85 2620.4,250 2644.1,248.28 2666.4,247 2701.1,245.01 3262.2,246.36 3292.4,229 3301.6,223.71 3308.4,214.47 \ +3313.3,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "genotype to genotype part association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.19 2596.7,251.79 2619.8,249.93 2643.8,248.22 2666.4,247 2711.5,244.57 3438.6,250.28 3478.4,229 3488.2,223.75 3495.9,\ +214.4 3501.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "genotype to genotype part association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.73 2596.4,251.75 2619.7,249.88 2643.7,248.18 2666.4,247 2720.2,244.2 3587.5,253.68 3635.4,229 3645.7,223.67 3653.9,213.99 \ +3659.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "genotype to genotype part association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.77 2596.1,251.72 2619.5,249.85 2643.7,248.16 2666.4,247 2697.4,245.42 3756.6,242.85 3784.4,229 3795.1,223.66 3803.8,\ +213.84 3810.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "genotype to genotype part association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2595.9,251.7 2619.3,249.83 2643.6,248.14 2666.4,247 2702.1,245.22 3922.3,244.72 3954.4,229 3965.3,223.69 3974.1,\ +213.87 3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "genotype to genotype part association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2595.6,251.69 2619.1,249.81 2643.5,248.12 2666.4,247 2706.6,245.03 4080.2,248.54 4115.4,229 4124.9,223.75 4131.9,\ +214.39 4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "genotype to genotype part association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.3,195.51 1679.7,251.79 1702.8,249.93 1726.8,248.22 1749.4,247 1771.9,245.79 2543.7,245.09 2559.4,229 2565.6,222.65 2565.4,\ -213.61 2562.9,204.95", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2595.3,251.69 2618.9,249.8 2643.4,248.11 2666.4,247 2688.7,245.92 4257.6,243.75 4274.4,229 4280.9,223.32 4283.4,\ +214.65 4284.1,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "genotype to genotype part association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.84 1679.7,251.77 1702.8,249.91 1726.8,248.21 1749.4,247 1796.7,244.47 2557.9,247.8 2601.4,229 2613.8,223.65 2624.6,\ -213.54 2632.9,203.81", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2595.3,251.69 2618.9,249.8 2643.4,248.11 2666.4,247 2712.3,244.78 4276.1,244.35 4319.4,229 4334.6,223.59 4349,212.83 \ +4360.1,202.68", style=solid]; predicate [height=0.5, - pos="2774.4,178", + pos="4506.4,178", width=1.5165]; "genotype to genotype part association" -> predicate [color=blue, label=predicate, - lp="2759.4,221.5", - pos="e,2754.4,194.99 1679.4,251.76 1702.7,249.89 1726.7,248.19 1749.4,247 1853.8,241.52 2589.8,257.7 2690.4,229 2710.3,223.32 2730.3,\ -211.69 2745.8,201.07", + lp="4485.4,221.5", + pos="e,4484.7,194.58 2595.3,251.68 2618.9,249.79 2643.4,248.1 2666.4,247 2763.3,242.35 4319.4,253.18 4413.4,229 4435.8,223.24 4458.7,\ +211.04 4476.1,200.13", style=solid]; subject [height=0.5, - pos="2891.4,178", + pos="4623.4,178", width=1.2277]; "genotype to genotype part association" -> subject [color=blue, label=subject, - lp="2861.4,221.5", - pos="e,2870.2,194.05 1679.1,251.74 1702.5,249.87 1726.7,248.17 1749.4,247 1865.7,241.02 2684.6,258.15 2797.4,229 2820.3,223.09 2843.7,\ -210.63 2861.5,199.63", + lp="4590.4,221.5", + pos="e,4601.1,193.87 2595.3,251.66 2618.9,249.78 2643.4,248.1 2666.4,247 2769.4,242.08 4423.1,253.19 4523.4,229 4547.9,223.09 4573.2,\ +210.33 4592.3,199.17", style=solid]; object [height=0.5, - pos="2934.4,91", + pos="4666.4,91", width=1.0832]; "genotype to genotype part association" -> object [color=blue, label=object, - lp="2984.4,178", - pos="e,2947.8,108.09 1678.9,251.74 1702.3,249.86 1726.6,248.16 1749.4,247 1812.8,243.78 2830.5,246.92 2891.4,229 2918,221.16 2928.2,218.5 \ -2944.4,196 2962.7,170.69 2966.3,156.9 2957.4,127 2956.4,123.55 2954.9,120.13 2953.1,116.85", + lp="4716.4,178", + pos="e,4679.8,108.09 2595.3,251.65 2618.9,249.77 2643.4,248.09 2666.4,247 2774.8,241.85 4515.8,258.05 4620.4,229 4648.2,221.27 4659.2,\ +219.22 4676.4,196 4695,170.92 4698.3,156.9 4689.4,127 4688.4,123.55 4686.9,120.13 4685.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1796.4,265", + pos="2713.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1927.4,265", + pos="2844.4,265", width=2.0762]; "genotype to genotype part association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2098.4,265", + pos="3015.4,265", width=2.1665]; subject -> object [label=relation, - lp="2929.4,134.5", - pos="e,2916.5,107.23 2892.5,159.55 2893.7,149.57 2896.2,137.07 2901.4,127 2903.6,122.68 2906.5,118.52 2909.7,114.66"]; + lp="4661.4,134.5", + pos="e,4648.5,107.23 4624.5,159.55 4625.7,149.57 4628.2,137.07 4633.4,127 4635.6,122.68 4638.5,118.52 4641.7,114.66"]; relation [height=0.5, - pos="2879.4,18", + pos="4611.4,18", width=1.2999]; - subject -> relation [pos="e,2880.7,36.188 2890.1,159.79 2888,132.48 2884,78.994 2881.5,46.38", + subject -> relation [pos="e,4612.7,36.188 4622.1,159.79 4620,132.48 4616,78.994 4613.5,46.38", style=dotted]; "genotype to genotype part association_subject" [color=blue, height=0.5, label=genotype, - pos="2248.4,265", + pos="3165.4,265", width=1.4985]; - object -> relation [pos="e,2892.2,35.54 2921.9,73.889 2915,64.939 2906.2,53.617 2898.4,43.584", + object -> relation [pos="e,4624.2,35.54 4653.9,73.889 4647,64.939 4638.2,53.617 4630.4,43.584", style=dotted]; "genotype to genotype part association_object" [color=blue, height=0.5, label=genotype, - pos="2374.4,265", + pos="3291.4,265", width=1.4985]; } diff --git a/graphviz/genotype_to_genotype_part_association.svg b/graphviz/genotype_to_genotype_part_association.svg index 081a9047ba..3602c6511a 100644 --- a/graphviz/genotype_to_genotype_part_association.svg +++ b/graphviz/genotype_to_genotype_part_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to genotype part association - -genotype to genotype part association + +genotype to genotype part association @@ -24,9 +24,9 @@ genotype to genotype part association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ genotype to genotype part association->id - - -id + + +id @@ -50,9 +50,9 @@ genotype to genotype part association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ genotype to genotype part association->name - - -name + + +name @@ -76,9 +76,9 @@ genotype to genotype part association->description - - -description + + +description @@ -89,9 +89,9 @@ genotype to genotype part association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genotype to genotype part association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genotype to genotype part association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genotype to genotype part association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ genotype to genotype part association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ genotype to genotype part association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ genotype to genotype part association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ genotype to genotype part association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ genotype to genotype part association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ genotype to genotype part association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ genotype to genotype part association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ genotype to genotype part association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +genotype to genotype part association->subject category + + +subject category + + + +object category + +ontology class + + + +genotype to genotype part association->object category + + +object category + + + +subject closure + +string + + + +genotype to genotype part association->subject closure + + +subject closure + + + +object closure + +string + + + +genotype to genotype part association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +genotype to genotype part association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +genotype to genotype part association->object category closure + + +object category closure + + + +subject namespace + +string + + + +genotype to genotype part association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +genotype to genotype part association->object namespace + + +object namespace + + + +subject label closure + +string + + + +genotype to genotype part association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +genotype to genotype part association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +genotype to genotype part association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + genotype to genotype part association->type - - -type + + +type - + category - -category + +category - + genotype to genotype part association->category - - -category + + +category - + predicate - -predicate + +predicate - + genotype to genotype part association->predicate - - -predicate + + +predicate - + subject - -subject + +subject - + genotype to genotype part association->subject - - -subject + + +subject - + object - -object + +object - + genotype to genotype part association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + genotype to genotype part association_predicate - -predicate type + +predicate type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + genotype to genotype part association_subject - -genotype + +genotype - + object->relation - - + + - + genotype to genotype part association_object - -genotype + +genotype diff --git a/graphviz/genotype_to_phenotypic_feature_association.gv b/graphviz/genotype_to_phenotypic_feature_association.gv index 120e6d5d32..e869673b2d 100644 --- a/graphviz/genotype_to_phenotypic_feature_association.gv +++ b/graphviz/genotype_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4926.4,283"]; + graph [bb="0,0,6597.4,283"]; node [label="\N"]; "genotype to phenotypic feature association" [height=0.5, label="genotype to phenotypic feature association", - pos="2911.4,265", + pos="3653.4,265", width=5.8675]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to phenotypic feature association" -> association [label=is_a, - lp="725.39,221.5", - pos="e,106.71,190.75 2700.5,263.53 2308.6,262.03 1441.5,255.67 711.39,229 454.7,219.62 388.58,232.99 134.39,196 128.61,195.16 122.61,\ -194.08 116.66,192.87"]; + lp="720.39,221.5", + pos="e,106.71,190.74 3443.6,262.76 2862.5,259.12 1240,247.55 706.39,229 451.9,220.15 386.38,232.73 134.39,196 128.61,195.16 122.61,194.08 \ +116.66,192.87"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "genotype to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, - lp="968.89,221.5", - pos="e,497.63,192.66 2700,264.89 2340.6,265.35 1587.9,261.8 952.39,229 800.19,221.14 626.22,205.41 507.83,193.68"]; + lp="960.89,221.5", + pos="e,495.26,192.8 3443.1,263.29 2894.6,261.1 1429.4,253.12 944.39,229 794,221.52 622.1,205.68 505.33,193.82"]; "genotype to entity association mixin" [height=0.5, pos="789.39,178", width=4.9829]; "genotype to phenotypic feature association" -> "genotype to entity association mixin" [label=uses, lp="1117.9,221.5", - pos="e,865.95,194.33 2700.5,263.62 2291.9,262.27 1405.7,256.19 1101.4,229 1024.8,222.16 938.52,207.81 876.14,196.24"]; + pos="e,865.3,194.33 3443.6,262.87 2875,259.57 1331.2,248.88 1101.4,229 1024.5,222.35 937.92,207.91 875.5,196.25"]; id [color=blue, height=0.5, label=string, @@ -32,7 +32,7 @@ digraph { "genotype to phenotypic feature association" -> id [color=blue, label=id, lp="1225.4,221.5", - pos="e,1054.4,189.89 2702.8,262.06 2282.5,257.81 1361.7,246.61 1218.4,229 1152.8,220.94 1136.9,214.4 1073.4,196 1070.3,195.1 1067.1,194.11 \ + pos="e,1054.4,189.89 3442.8,263.5 2891.9,261.83 1435.5,254.98 1218.4,229 1152.8,221.15 1136.9,214.4 1073.4,196 1070.3,195.1 1067.1,194.11 \ 1063.9,193.08", style=solid]; iri [color=blue, @@ -43,7 +43,7 @@ digraph { "genotype to phenotypic feature association" -> iri [color=blue, label=iri, lp="1313.4,221.5", - pos="e,1158.2,190.67 2702.7,262.18 2299.2,258.26 1439.9,247.81 1305.4,229 1257.2,222.26 1203.7,206.11 1167.8,193.97", + pos="e,1158.2,190.74 3442.5,263.76 2905.3,262.74 1513.3,257.35 1305.4,229 1257.2,222.42 1203.6,206.24 1167.8,194.06", style=solid]; name [color=blue, height=0.5, @@ -53,7 +53,7 @@ digraph { "genotype to phenotypic feature association" -> name [color=blue, label=name, lp="1397.4,221.5", - pos="e,1274.7,193.4 2701,263.15 2310.9,260.99 1503.5,253.58 1377.4,229 1344.9,222.66 1309.9,209.07 1284.1,197.65", + pos="e,1274.7,193.47 3443.7,262.74 2899.6,259.19 1477.7,248.16 1377.4,229 1344.8,222.78 1309.9,209.18 1284.1,197.73", style=solid]; description [color=blue, height=0.5, @@ -63,7 +63,7 @@ digraph { "genotype to phenotypic feature association" -> description [color=blue, label=description, lp="1481.9,221.5", - pos="e,1405.9,196.3 2701,263.32 2308.2,261.43 1497.6,254.47 1441.4,229 1429.8,223.73 1419.7,213.97 1412,204.47", + pos="e,1405.5,195.84 3443.3,262.86 2899.9,259.63 1486.7,249.29 1441.4,229 1429.6,223.7 1419.4,213.75 1411.7,204.1", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,18 +73,18 @@ digraph { "genotype to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1578.4,221.5", - pos="e,1530.8,196 2702.1,262.42 2321.2,259.03 1551.5,249.64 1531.4,229 1525.4,222.83 1525.3,214.08 1527.4,205.62", + pos="e,1530.8,196.02 3442.1,264.39 2911.9,264.86 1564.6,262.74 1531.4,229 1525.3,222.85 1525.2,214.11 1527.4,205.65", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="3717.4,91", + pos="5388.4,91", width=1.9318]; "genotype to phenotypic feature association" -> object [color=blue, label=object, lp="1659.4,178", - pos="e,3648,92.956 2700.3,264.26 2486.8,262.82 2147.5,255.86 1855.4,229 1754.2,219.7 1566.7,233.03 1637.4,160 1672.8,123.4 3260.8,98.503 \ -3637.7,93.102", + pos="e,5318.6,91.92 3442.8,263.42 3035.9,261.72 2155.1,255.06 1852.4,229 1752.4,220.39 1567.1,231.6 1637.4,160 1704,92.178 4770.1,91.507 \ +5308.2,91.912", style=solid]; negated [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=1.2999]; "genotype to phenotypic feature association" -> negated [color=blue, label=negated, - lp="1965.4,221.5", - pos="e,1771.8,190.23 2704.9,261.17 2463.7,257.06 2079.4,247.78 1936.4,229 1882.2,221.88 1821.4,205.32 1781.5,193.21", + lp="1960.4,221.5", + pos="e,1771.2,190.49 3444.4,262.25 3018.5,258.3 2077.5,247.61 1931.4,229 1878.8,222.3 1820.1,205.86 1781.2,193.65", style=solid]; qualifiers [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=2.1304]; "genotype to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2098.9,221.5", - pos="e,1920.5,193.12 2705.9,260.68 2495.9,256.35 2184.1,247.1 2065.4,229 2018.9,221.91 1967.3,207.62 1930.1,196.13", + lp="2099.9,221.5", + pos="e,1920,193.12 3444.4,262.16 3044.6,258.23 2198.9,247.81 2066.4,229 2019.3,222.31 1967.1,207.84 1929.7,196.18", style=solid]; publications [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=1.7332]; "genotype to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2237.4,221.5", - pos="e,2070.5,192.99 2708.3,259.92 2531.3,255.3 2288.5,246.07 2193.4,229 2154.3,221.98 2111.4,207.99 2080.2,196.59", + lp="2246.4,221.5", + pos="e,2071.2,192.77 3444.7,262.04 3072.4,258.09 2321.4,247.9 2202.4,229 2160.2,222.3 2113.8,207.8 2080.7,196.13", style=solid]; "has evidence" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=2.0943]; "genotype to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2384.9,221.5", - pos="e,2226.6,193.95 2718,257.7 2580.7,252.17 2408.7,242.84 2338.4,229 2303.1,222.05 2264.7,208.76 2236,197.63", + lp="2406.9,221.5", + pos="e,2230,193.56 3442,264.94 3130.2,265.2 2562.2,261.01 2360.4,229 2318.7,222.39 2272.9,208.39 2239.5,196.89", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "genotype to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2525.9,221.5", - pos="e,2410.5,195.85 2711.6,259.15 2613.5,254.63 2506.8,245.89 2461.4,229 2445.7,223.15 2430.4,212.52 2418.3,202.57", + lp="2563.9,221.5", + pos="e,2420.6,195.66 3444.3,262.28 3136.6,259.04 2588.3,250.33 2499.4,229 2475,223.14 2449.5,211.3 2429.6,200.62", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -143,8 +143,8 @@ digraph { width=3.015]; "genotype to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2692.4,221.5", - pos="e,2607.3,195.76 2739.7,254.5 2672.1,248.97 2607.9,240.73 2597.4,229 2590.5,221.31 2593.9,211.9 2600.5,203.32", + lp="2737.4,221.5", + pos="e,2628.3,196.18 3443.3,263 3156.3,260.74 2673.3,253.31 2642.4,229 2635.4,223.47 2631.7,214.72 2629.8,206.08", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -153,8 +153,8 @@ digraph { width=3.015]; "genotype to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2900.9,221.5", - pos="e,2816.7,194.29 2818.1,248.85 2808.9,243.89 2800.7,237.42 2794.4,229 2785.6,217.21 2794,207.04 2807.7,199.01", + lp="2946.9,221.5", + pos="e,2846.7,195.94 3444.8,262.12 3210.8,258.95 2861.1,250.62 2840.4,229 2833.8,222.07 2835.9,212.87 2840.9,204.26", style=solid]; timepoint [color=blue, height=0.5, @@ -163,8 +163,8 @@ digraph { width=1.5346]; "genotype to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3057.4,221.5", - pos="e,3036,195.86 2972.4,247.7 2984.7,242.83 2997,236.68 3007.4,229 3016.3,222.4 3024.2,213.12 3030.4,204.35", + lp="3104.4,221.5", + pos="e,3049,196.35 3445.5,261.75 3290.6,258.37 3100.6,249.94 3069.4,229 3061.4,223.62 3056,214.78 3052.3,206.02", style=solid]; "original subject" [color=blue, height=0.5, @@ -173,8 +173,8 @@ digraph { width=1.0652]; "genotype to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3176.4,221.5", - pos="e,3142.4,195.02 3032.1,250.2 3054.1,245.18 3076.4,238.33 3096.4,229 3110.6,222.38 3124.2,211.71 3135,201.92", + lp="3204.4,221.5", + pos="e,3147.9,195.88 3443.6,262.68 3314.2,259.61 3169.1,251.17 3148.4,229 3142.5,222.7 3142.4,213.92 3144.6,205.47", style=solid]; "original predicate" [color=blue, height=0.5, @@ -183,8 +183,8 @@ digraph { width=1.5887]; "genotype to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3315.9,221.5", - pos="e,3263.9,195.85 3067.5,252.83 3142.8,246.41 3220.1,237.88 3235.4,229 3245.1,223.35 3252.9,213.92 3258.7,204.77", + lp="3333.9,221.5", + pos="e,3265.7,195.91 3460.3,257.66 3372.1,252.73 3284.2,244.07 3270.4,229 3264.8,222.87 3263.5,214.34 3264.1,206.06", style=solid]; "original object" [color=blue, height=0.5, @@ -193,162 +193,277 @@ digraph { width=1.0652]; "genotype to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3441.9,221.5", - pos="e,3389.9,196.07 3061.8,252.33 3085.4,250.52 3109.6,248.7 3132.4,247 3160.3,244.93 3363.9,249.08 3383.4,229 3389.2,223.03 3390.9,\ -214.55 3390.8,206.26", + lp="3465.9,221.5", + pos="e,3390.9,196.13 3502.6,252.37 3464.6,247.13 3430.1,239.64 3414.4,229 3406,223.3 3399.7,214.27 3395.1,205.45", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3518.4,178", + width=2.1304]; + "genotype to phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3587.9,221.5", + pos="e,3517.5,196.32 3556.6,248.97 3546.1,244.01 3536.3,237.51 3528.4,229 3522.7,222.88 3519.9,214.5 3518.5,206.34", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3689.4,178", + width=2.1304]; + "genotype to phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3709.9,221.5", + pos="e,3667.8,195.45 3650.6,246.67 3649.8,236.72 3650,224.22 3654.4,214 3656.1,210.09 3658.4,206.38 3661.1,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3822.4,178", + width=1.0652]; + "genotype to phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="3840.9,221.5", + pos="e,3807.8,194.94 3721,247.86 3736.1,242.9 3751.7,236.68 3765.4,229 3778.1,221.88 3790.4,211.6 3800.4,202.2", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3918.4,178", + width=1.0652]; + "genotype to phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="3959.4,221.5", + pos="e,3915.7,196.01 3813.1,253.21 3850,248.03 3882.7,240.35 3897.4,229 3904.8,223.29 3909.6,214.5 3912.7,205.87", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4051.4,178", + width=2.1304]; + "genotype to phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4117.9,221.5", + pos="e,4043.3,195.91 3802.5,252.23 3897.2,244.3 4003.8,234.35 4013.4,229 4023.5,223.36 4031.8,213.81 4038,204.56", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4240.4,178", + width=2.1304]; + "genotype to phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4307.9,221.5", + pos="e,4234.6,196.01 3801.4,252.14 3825.8,250.33 3850.8,248.54 3874.4,247 3911.6,244.57 4177.3,248 4209.4,229 4218.5,223.59 4225.4,214.34 \ +4230.2,205.25", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4430.4,178", + width=1.0652]; + "genotype to phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4480.4,221.5", + pos="e,4423.4,196.14 3799,251.92 3824.1,250.09 3850,248.36 3874.4,247 3903.3,245.39 4369.9,242.82 4395.4,229 4405.2,223.69 4412.8,214.33 \ +4418.4,205.13", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4589.4,178", + width=1.0652]; + "genotype to phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4633.4,221.5", + pos="e,4582,195.7 3797.8,251.85 3823.3,250 3849.6,248.28 3874.4,247 3912,245.05 4519,246.4 4552.4,229 4562.7,223.63 4570.9,213.94 4576.9,\ +204.51", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4740.4,178", + width=1.0652]; + "genotype to phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4793.4,221.5", + pos="e,4732.4,195.74 3797.2,251.79 3822.9,249.93 3849.4,248.23 3874.4,247 3920.3,244.74 4660.3,249.61 4701.4,229 4712.1,223.63 4720.7,\ +213.81 4727.1,204.28", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4869.4,178", + width=1.0652]; + "genotype to phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="4947.9,221.5", + pos="e,4875.8,196.1 3796.6,251.75 3822.5,249.89 3849.2,248.19 3874.4,247 3902.1,245.69 4852,248.76 4871.4,229 4877.3,223.01 4878.4,214.41 \ +4877.6,206.03", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5010.4,178", + width=2.347]; + "genotype to phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5096.9,221.5", + pos="e,5021,195.98 3796.3,251.73 3822.3,249.86 3849.1,248.17 3874.4,247 3906.2,245.53 4999,251.71 5021.4,229 5027.6,222.74 5027.3,213.86 \ +5024.7,205.32", style=solid]; type [height=0.5, - pos="3473.4,178", + pos="5144.4,178", width=0.86659]; "genotype to phenotypic feature association" -> type [color=blue, label=type, - lp="3518.4,221.5", - pos="e,3489,194.02 3058.8,252.1 3083.3,250.27 3108.6,248.5 3132.4,247 3152.7,245.72 3483.4,243.71 3497.4,229 3504.6,221.42 3501.4,211.26 \ -3495.3,202.08", + lp="5191.4,221.5", + pos="e,5160.7,193.58 3796,251.71 3822,249.84 3849,248.15 3874.4,247 3892.4,246.18 5157.8,241.82 5170.4,229 5178,221.24 5174.1,210.77 \ +5167.2,201.41", style=solid]; category [height=0.5, - pos="3574.4,178", + pos="5245.4,178", width=1.4263]; "genotype to phenotypic feature association" -> category [color=blue, label=category, - lp="3586.9,221.5", - pos="e,3567,196.11 3058.2,252.04 3082.9,250.21 3108.4,248.46 3132.4,247 3177.5,244.27 3498.7,250.47 3538.4,229 3548.4,223.6 3556.3,214.09 \ -3562.1,204.8", + lp="5258.9,221.5", + pos="e,5238.8,196.21 3796,251.7 3822,249.83 3849,248.15 3874.4,247 3911.5,245.32 5178.7,246.6 5211.4,229 5221.1,223.78 5228.6,214.43 \ +5234,205.22", style=solid]; predicate [height=0.5, - pos="3698.4,178", + pos="5369.4,178", width=1.5165]; "genotype to phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="3688.4,221.5", - pos="e,3680.2,195.12 3057.3,251.95 3082.3,250.12 3108.1,248.38 3132.4,247 3186.8,243.91 3570.5,245.58 3622.4,229 3640.5,223.23 3658.3,\ -211.87 3672.1,201.44", + lp="5360.4,221.5", + pos="e,5351.5,195.26 3796,251.68 3822,249.82 3849,248.14 3874.4,247 3953.2,243.47 5219,252.34 5294.4,229 5312.3,223.44 5330,212.1 5343.6,\ +201.62", style=solid]; subject [height=0.5, - pos="3815.4,178", + pos="5486.4,178", width=1.2277]; "genotype to phenotypic feature association" -> subject [color=blue, label=subject, - lp="3789.4,221.5", - pos="e,3795.1,194.2 3056.4,251.88 3081.7,250.04 3107.8,248.32 3132.4,247 3198.3,243.47 3662.8,246.68 3726.4,229 3747.9,223.03 3769.7,\ -210.87 3786.4,200.03", + lp="5460.4,221.5", + pos="e,5466.4,194.32 3795.7,251.69 3821.8,249.81 3848.9,248.13 3874.4,247 3959,243.25 5316.7,251.12 5398.4,229 5419.7,223.23 5441.3,211.07 \ +5457.8,200.19", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3962.4,178", + pos="5633.4,178", width=2.3651]; "genotype to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3944.4,221.5", - pos="e,3927.7,194.56 3055.8,251.84 3081.3,249.99 3107.6,248.28 3132.4,247 3284.9,239.14 3669.2,256.53 3819.4,229 3853.5,222.74 3890.5,\ -209.65 3918.2,198.44", + lp="5615.4,221.5", + pos="e,5599,194.6 3795.7,251.67 3821.8,249.8 3848.9,248.12 3874.4,247 4053.8,239.11 5313.5,260.04 5490.4,229 5524.7,222.98 5561.8,209.81 \ +5589.6,198.5", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4141.4,178", + pos="5812.4,178", width=2.1123]; "genotype to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4127.4,221.5", - pos="e,4111.3,194.63 3054.9,251.78 3080.7,249.92 3107.3,248.22 3132.4,247 3230.5,242.23 3920.1,248.56 4016.4,229 4046.2,222.94 4078,210.11 \ -4102.1,198.96", + lp="5798.4,221.5", + pos="e,5782.5,194.61 3795.4,251.67 3821.6,249.79 3848.8,248.11 3874.4,247 3975,242.63 5588.6,248.54 5687.4,229 5717.4,223.08 5749.3,210.17 \ +5773.4,198.96", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4271.4,178", + pos="5942.4,178", width=1.011]; "genotype to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4276.9,221.5", - pos="e,4254,194.03 3054.6,251.73 3080.5,249.87 3107.2,248.18 3132.4,247 3191.2,244.24 4136,245.88 4192.4,229 4211.9,223.17 4231.2,211.05 \ -4245.9,200.21", + lp="5947.9,221.5", + pos="e,5925,194.08 3795.4,251.65 3821.6,249.77 3848.8,248.1 3874.4,247 3929.6,244.63 5810.4,244.62 5863.4,229 5882.9,223.25 5902.3,211.13 \ +5916.9,200.27", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="4399.4,178", + pos="6070.4,178", width=2.0401]; "genotype to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="4405.4,221.5", - pos="e,4383.2,195.72 3054.3,251.71 3080.2,249.85 3107.1,248.16 3132.4,247 3199,243.94 4269.3,250.48 4332.4,229 4348.4,223.57 4363.6,212.77 \ -4375.6,202.59", + lp="6076.4,221.5", + pos="e,6054.3,195.75 3795.4,251.64 3821.6,249.76 3848.8,248.09 3874.4,247 3933.5,244.48 5947.3,247.87 6003.4,229 6019.4,223.62 6034.7,\ +212.82 6046.6,202.64", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="4535.4,178", + pos="6206.4,178", width=1.2277]; "genotype to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="4522.4,221.5", - pos="e,4516.6,194.54 3054,251.7 3080,249.83 3107,248.15 3132.4,247 3205.7,243.68 4382.9,249.33 4453.4,229 4473.2,223.29 4493,211.42 4508.2,\ -200.68", + lp="6193.4,221.5", + pos="e,6187.6,194.58 3795.1,251.65 3821.4,249.77 3848.7,248.09 3874.4,247 3936.8,244.35 6064.3,246.14 6124.4,229 6144.2,223.34 6164,211.48 \ +6179.2,200.72", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="4641.4,178", + pos="6312.4,178", width=1.2277]; "genotype to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="4625.9,221.5", - pos="e,4623.1,194.54 3054,251.68 3080,249.81 3107,248.13 3132.4,247 3211.7,243.45 4485.2,251.37 4561.4,229 4580.8,223.29 4600.2,211.42 \ -4615,200.68", + lp="6296.9,221.5", + pos="e,6294.1,194.57 3795.1,251.64 3821.4,249.76 3848.7,248.08 3874.4,247 3939.8,244.24 6169.5,247.3 6232.4,229 6251.9,223.34 6271.2,\ +211.47 6286,200.72", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="4745.4,178", + pos="6416.4,178", width=1.1735]; "genotype to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="4741.4,221.5", - pos="e,4726.4,194.31 3053.7,251.69 3079.8,249.81 3106.9,248.13 3132.4,247 3217.3,243.24 4579.6,252.01 4661.4,229 4681.9,223.22 4702.6,\ -211.06 4718.2,200.18", + lp="6412.4,221.5", + pos="e,6397.4,194.34 3795.1,251.63 3821.4,249.75 3848.7,248.08 3874.4,247 3942.6,244.13 6266.6,247.35 6332.4,229 6352.9,223.27 6373.6,\ +211.1 6389.2,200.21", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4852.4,178", + pos="6523.4,178", width=1.1735]; "genotype to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="4871.4,221.5", - pos="e,4837.9,195.47 3053.7,251.67 3079.8,249.79 3106.9,248.12 3132.4,247 3178.4,244.98 4747,244.57 4790.4,229 4805.5,223.58 4819.6,212.83 \ -4830.6,202.67", + lp="6542.4,221.5", + pos="e,6509.4,195 3795.1,251.63 3821.4,249.75 3848.7,248.08 3874.4,247 3946.2,243.99 6393.7,253.16 6461.4,229 6476.7,223.54 6491,212.56 \ +6502,202.28", style=solid]; relation [height=0.5, - pos="3766.4,18", + pos="5437.4,18", width=1.2999]; - object -> relation [pos="e,3754.9,35.705 3729,73.174 3735,64.509 3742.4,53.768 3749,44.141", + object -> relation [pos="e,5425.9,35.705 5400,73.174 5406,64.509 5413.4,53.768 5420,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3179.4,265", + pos="3921.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3310.4,265", + pos="4052.4,265", width=2.0762]; "genotype to phenotypic feature association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3481.4,265", + pos="4223.4,265", width=2.1665]; subject -> object [label=relation, - lp="3773.4,134.5", - pos="e,3723.8,108.97 3782.9,165.59 3770.1,159.94 3756,152.13 3745.4,142 3738.4,135.31 3732.7,126.48 3728.3,118.1"]; - subject -> relation [pos="e,3777.6,35.828 3814,159.99 3811.9,139.02 3807,102.55 3796.4,73 3792.9,63.258 3787.8,53.189 3782.8,44.423", + lp="5444.4,134.5", + pos="e,5394.8,108.97 5453.9,165.59 5441.1,159.94 5427,152.13 5416.4,142 5409.4,135.31 5403.7,126.48 5399.3,118.1"]; + subject -> relation [pos="e,5448.6,35.828 5485,159.99 5482.9,139.02 5478,102.55 5467.4,73 5463.9,63.258 5458.8,53.189 5453.8,44.423", style=dotted]; "genotype to phenotypic feature association_subject" [color=blue, height=0.5, label=genotype, - pos="3631.4,265", + pos="4373.4,265", width=1.4985]; } diff --git a/graphviz/genotype_to_phenotypic_feature_association.svg b/graphviz/genotype_to_phenotypic_feature_association.svg index 2d72eb4210..62460622d8 100644 --- a/graphviz/genotype_to_phenotypic_feature_association.svg +++ b/graphviz/genotype_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to phenotypic feature association - -genotype to phenotypic feature association + +genotype to phenotypic feature association @@ -24,9 +24,9 @@ genotype to phenotypic feature association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ genotype to phenotypic feature association->entity to phenotypic feature association mixin - - -uses + + +uses @@ -50,8 +50,8 @@ genotype to phenotypic feature association->genotype to entity association mixin - - + + uses @@ -63,7 +63,7 @@ genotype to phenotypic feature association->id - + id @@ -76,8 +76,8 @@ genotype to phenotypic feature association->iri - - + + iri @@ -89,8 +89,8 @@ genotype to phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ genotype to phenotypic feature association->description - - + + description @@ -115,21 +115,21 @@ genotype to phenotypic feature association->has attribute - - + + has attribute object - -named thing + +named thing genotype to phenotypic feature association->object - - + + object @@ -141,9 +141,9 @@ genotype to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ genotype to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ genotype to phenotypic feature association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ genotype to phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ genotype to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ genotype to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ genotype to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ genotype to phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -245,9 +245,9 @@ genotype to phenotypic feature association->original subject - - -original subject + + +original subject @@ -258,9 +258,9 @@ genotype to phenotypic feature association->original predicate - - -original predicate + + +original predicate @@ -271,214 +271,357 @@ genotype to phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +genotype to phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +genotype to phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +genotype to phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +genotype to phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +genotype to phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +genotype to phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +genotype to phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +genotype to phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +genotype to phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +genotype to phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +genotype to phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + genotype to phenotypic feature association->type - - -type + + +type - + category - -category + +category - + genotype to phenotypic feature association->category - - -category + + +category - + predicate - -predicate + +predicate - + genotype to phenotypic feature association->predicate - - -predicate + + +predicate - + subject - -subject + +subject - + genotype to phenotypic feature association->subject - - -subject + + +subject - + frequency qualifier - -frequency value + +frequency value - + genotype to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + genotype to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + genotype to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier - + sex qualifier - -biological sex + +biological sex - + genotype to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier - + has count - -integer + +integer - + genotype to phenotypic feature association->has count - - -has count + + +has count - + has total - -integer + +integer - + genotype to phenotypic feature association->has total - - -has total + + +has total - + has quotient - -double + +double - + genotype to phenotypic feature association->has quotient - - -has quotient + + +has quotient - + has percentage - -double + +double - + genotype to phenotypic feature association->has percentage - - -has percentage + + +has percentage - + relation - -relation + +relation - + object->relation - - + + - + association_type - -string + +string - + association_category - -category type + +category type - + genotype to phenotypic feature association_predicate - -predicate type + +predicate type - + subject->object - - -relation + + +relation - + subject->relation - - + + - + genotype to phenotypic feature association_subject - -genotype + +genotype diff --git a/graphviz/genotype_to_variant_association.gv b/graphviz/genotype_to_variant_association.gv index 5dc42aaf16..246fd4166f 100644 --- a/graphviz/genotype_to_variant_association.gv +++ b/graphviz/genotype_to_variant_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3006.4,283"]; + graph [bb="0,0,4738.4,283"]; node [label="\N"]; "genotype to variant association" [height=0.5, label="genotype to variant association", - pos="1551.4,265", + pos="2468.4,265", width=4.351]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to variant association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1395,263.85 1102.1,262.89 481.46,257.44 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2312.2,263.54 1843.2,261.89 467.2,254.87 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "genotype to variant association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1396.2,262.55 1126.6,259.49 582.79,250.76 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2312.6,263.05 1862.2,260.09 578.21,249.88 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "genotype to variant association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1397.1,261.68 1150.5,257.49 678.18,247.33 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2312.6,262.83 1879,259.34 678.94,248.07 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "genotype to variant association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1396.8,262.07 1168.4,258.56 751.85,249.54 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2312.5,263.16 1893.7,260.6 763.8,251.66 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "genotype to variant association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1395.7,262.8 1187.6,260.3 830.05,252.6 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2312.1,263.7 1908.6,262.52 852.7,256.78 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genotype to variant association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1397.3,261.69 1220.1,258.11 940.58,249.37 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2312.3,263.52 1931.9,261.95 977.72,255.39 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genotype to variant association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1398,261.32 1287.9,257.66 1136.3,249.07 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2311.7,264.31 1988.4,264.29 1257.1,260.62 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genotype to variant association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1403.6,258.92 1322,254.33 1219,245.6 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2311.7,264.36 2011.6,264.29 1366,260.36 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genotype to variant association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1419.1,255.36 1365.9,250.16 1304.2,241.93 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2311.6,264.32 2036.1,264.06 1475.8,259.61 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "genotype to variant association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1462.8,250.03 1435.4,244.66 1405.4,237.69 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2311.7,263.61 2065.3,262.18 1598.4,255.86 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "genotype to variant association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1506.6,247.63 1497.9,242.75 1489.6,236.61 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2314.4,261.46 2076.8,257.03 1641.1,246.61 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "genotype to variant association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.4,247.25 1591.3,241.57 1602.4,235.12 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2313.9,261.79 2099.2,258 1734.4,248.7 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "genotype to variant association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1662.1,252.23 1731.2,244.47 1809.8,234.72 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,\ -202.83 1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2318.8,259.65 2158,254.23 1923.3,243.83 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "genotype to variant association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.19 1660.7,252.02 1679.6,250.18 1699.1,248.42 1717.4,247 1793.7,241.1 1990.1,256.93 2061.4,229 2069.3,225.89 2084,213.75 \ -2096.8,202.21", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2329.8,256.56 2245.7,250.8 2151.7,241.67 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "genotype to variant association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1659.8,251.94 1679,250.08 1698.8,248.34 1717.4,247 1814.3,240.05 2061.8,258.61 2154.4,229 2166,225.28 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2318.4,259.72 2272,255.01 2229.2,245.99 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "genotype to variant association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.5 1658.9,251.87 1678.3,250 1698.5,248.27 1717.4,247 1780.8,242.76 2230.1,252.08 2289.4,229 2297.1,225.98 2311.2,213.98 \ -2323.5,202.5", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2381.5,249.91 2359.9,244.58 2341.1,237.66 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "genotype to variant association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.43 1658.4,251.81 1678,249.93 1698.3,248.21 1717.4,247 1757.4,244.45 2406.1,251.34 2439.4,229 2447.3,223.7 2452.4,214.89 \ -2455.6,206.12", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "genotype to variant association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2539.6,248.91 2551.5,244.01 2563,237.55 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "genotype to variant association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2584.9,252.92 2633.8,247.03 2684.4,238.93 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "genotype to variant association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.55 2580,252.31 2598.2,250.48 2616.8,248.65 2634.4,247 2681.2,242.6 2802.4,248.22 2845.4,229 2858.3,223.21 2870.1,212.91 \ +2879.2,203.16", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "genotype to variant association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2997,196.24 2577.7,252.02 2596.6,250.17 2616.1,248.42 2634.4,247 2672.8,244.04 2949.5,251.95 2980.4,229 2987.7,223.55 2992.1,214.81 \ +2994.7,206.16", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "genotype to variant association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.12 2576.4,251.95 2595.7,250.08 2615.6,248.33 2634.4,247 2685.6,243.38 3051.3,253.61 3096.4,229 3106.2,223.67 3113.8,\ +214.3 3119.4,205.1", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "genotype to variant association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.11 2575.5,251.85 2595,249.96 2615.3,248.24 2634.4,247 2670.9,244.64 3260.7,247.22 3292.4,229 3301.6,223.71 3308.4,214.48 \ +3313.3,205.38", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "genotype to variant association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.19 2575,251.8 2594.7,249.91 2615.2,248.19 2634.4,247 2681.2,244.11 3437,251.1 3478.4,229 3488.2,223.76 3495.9,214.4 \ +3501.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "genotype to variant association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.74 2575,251.74 2594.7,249.86 2615.2,248.16 2634.4,247 2689.9,243.66 3586,254.48 3635.4,229 3645.7,223.68 3653.9,213.99 \ +3659.9,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "genotype to variant association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.77 2574.6,251.75 2594.4,249.85 2615,248.14 2634.4,247 2666.3,245.12 3755.8,243.24 3784.4,229 3795.1,223.66 3803.8,213.84 \ +3810.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "genotype to variant association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2574.5,251.72 2594.4,249.82 2615,248.12 2634.4,247 2671,244.88 3921.5,245.11 3954.4,229 3965.3,223.69 3974.1,213.87 \ +3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "genotype to variant association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2574.5,251.7 2594.4,249.8 2615,248.11 2634.4,247 2675.5,244.65 4079.4,248.97 4115.4,229 4124.9,223.75 4131.9,214.39 \ +4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "genotype to variant association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.3,195.51 1658,251.8 1677.7,249.91 1698.2,248.19 1717.4,247 1740.7,245.56 2543,245.72 2559.4,229 2565.6,222.66 2565.4,213.61 \ -2562.9,204.96", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2574.5,251.68 2594.4,249.78 2615,248.1 2634.4,247 2657.1,245.71 4257.3,244.04 4274.4,229 4280.9,223.32 4283.4,214.65 \ +4284.1,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "genotype to variant association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.84 1658,251.78 1677.7,249.89 1698.2,248.18 1717.4,247 1766.4,244 2556.3,248.49 2601.4,229 2613.8,223.65 2624.6,213.55 \ -2632.9,203.82", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2574.1,251.71 2594.1,249.8 2614.9,248.1 2634.4,247 2681.1,244.36 4275.3,244.64 4319.4,229 4334.6,223.59 4349,212.84 \ +4360.1,202.68", style=solid]; predicate [height=0.5, - pos="2774.4,178", + pos="4506.4,178", width=1.5165]; "genotype to variant association" -> predicate [color=blue, label=predicate, - lp="2759.4,221.5", - pos="e,2754.4,195 1658,251.75 1677.7,249.87 1698.2,248.16 1717.4,247 1825.3,240.49 2586.4,258.64 2690.4,229 2710.3,223.32 2730.3,211.69 \ -2745.8,201.08", + lp="4485.4,221.5", + pos="e,4484.7,194.58 2574.1,251.71 2594.1,249.8 2614.9,248.1 2634.4,247 2733.1,241.46 4317.7,253.62 4413.4,229 4435.8,223.25 4458.7,211.04 \ +4476.1,200.13", style=solid]; subject [height=0.5, - pos="2891.4,178", + pos="4623.4,178", width=1.2277]; "genotype to variant association" -> subject [color=blue, label=subject, - lp="2861.4,221.5", - pos="e,2870.2,194.05 1658,251.72 1677.7,249.84 1698.2,248.14 1717.4,247 1837.2,239.88 2681.2,259.01 2797.4,229 2820.3,223.1 2843.7,210.64 \ -2861.5,199.63", + lp="4590.4,221.5", + pos="e,4601.1,193.87 2574.1,251.7 2594.1,249.79 2614.9,248.09 2634.4,247 2739.2,241.15 4421.4,253.6 4523.4,229 4547.9,223.1 4573.2,210.33 \ +4592.3,199.18", style=solid]; object [height=0.5, - pos="2934.4,91", + pos="4666.4,91", width=1.0832]; "genotype to variant association" -> object [color=blue, label=object, - lp="2984.4,178", - pos="e,2947.8,108.09 1657.6,251.75 1677.4,249.85 1698,248.14 1717.4,247 1782.5,243.17 2828.8,247.41 2891.4,229 2918,221.17 2928.2,218.5 \ -2944.4,196 2962.7,170.69 2966.3,156.9 2957.4,127 2956.4,123.55 2954.9,120.13 2953.1,116.85", + lp="4716.4,178", + pos="e,4679.8,108.09 2574.1,251.69 2594.1,249.78 2614.9,248.09 2634.4,247 2744.6,240.87 4514.1,258.51 4620.4,229 4648.2,221.27 4659.2,\ +219.22 4676.4,196 4695,170.92 4698.3,156.9 4689.4,127 4688.4,123.55 4686.9,120.13 4685.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1764.4,265", + pos="2681.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1895.4,265", + pos="2812.4,265", width=2.0762]; "genotype to variant association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2066.4,265", + pos="2983.4,265", width=2.1665]; subject -> object [label=relation, - lp="2929.4,134.5", - pos="e,2916.5,107.23 2892.5,159.55 2893.7,149.57 2896.2,137.07 2901.4,127 2903.6,122.68 2906.5,118.52 2909.7,114.66"]; + lp="4661.4,134.5", + pos="e,4648.5,107.23 4624.5,159.55 4625.7,149.57 4628.2,137.07 4633.4,127 4635.6,122.68 4638.5,118.52 4641.7,114.66"]; relation [height=0.5, - pos="2879.4,18", + pos="4611.4,18", width=1.2999]; - subject -> relation [pos="e,2880.7,36.188 2890.1,159.79 2888,132.48 2884,78.994 2881.5,46.38", + subject -> relation [pos="e,4612.7,36.188 4622.1,159.79 4620,132.48 4616,78.994 4613.5,46.38", style=dotted]; "genotype to variant association_subject" [color=blue, height=0.5, label=genotype, - pos="2216.4,265", + pos="3133.4,265", width=1.4985]; - object -> relation [pos="e,2892.2,35.54 2921.9,73.889 2915,64.939 2906.2,53.617 2898.4,43.584", + object -> relation [pos="e,4624.2,35.54 4653.9,73.889 4647,64.939 4638.2,53.617 4630.4,43.584", style=dotted]; "genotype to variant association_object" [color=blue, height=0.5, label="sequence variant", - pos="2378.4,265", + pos="3295.4,265", width=2.5095]; } diff --git a/graphviz/genotype_to_variant_association.svg b/graphviz/genotype_to_variant_association.svg index fc5fd9f2a7..75cc3cd647 100644 --- a/graphviz/genotype_to_variant_association.svg +++ b/graphviz/genotype_to_variant_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to variant association - -genotype to variant association + +genotype to variant association @@ -24,9 +24,9 @@ genotype to variant association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ genotype to variant association->id - - -id + + +id @@ -50,9 +50,9 @@ genotype to variant association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ genotype to variant association->name - - -name + + +name @@ -76,9 +76,9 @@ genotype to variant association->description - - -description + + +description @@ -89,9 +89,9 @@ genotype to variant association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genotype to variant association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genotype to variant association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genotype to variant association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ genotype to variant association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ genotype to variant association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ genotype to variant association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ genotype to variant association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ genotype to variant association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ genotype to variant association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ genotype to variant association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ genotype to variant association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +genotype to variant association->subject category + + +subject category + + + +object category + +ontology class + + + +genotype to variant association->object category + + +object category + + + +subject closure + +string + + + +genotype to variant association->subject closure + + +subject closure + + + +object closure + +string + + + +genotype to variant association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +genotype to variant association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +genotype to variant association->object category closure + + +object category closure + + + +subject namespace + +string + + + +genotype to variant association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +genotype to variant association->object namespace + + +object namespace + + + +subject label closure + +string + + + +genotype to variant association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +genotype to variant association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +genotype to variant association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + genotype to variant association->type - - -type + + +type - + category - -category + +category - + genotype to variant association->category - - -category + + +category - + predicate - -predicate + +predicate - + genotype to variant association->predicate - - -predicate + + +predicate - + subject - -subject + +subject - + genotype to variant association->subject - - -subject + + +subject - + object - -object + +object - + genotype to variant association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + genotype to variant association_predicate - -predicate type + +predicate type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + genotype to variant association_subject - -genotype + +genotype - + object->relation - - + + - + genotype to variant association_object - -sequence variant + +sequence variant diff --git a/graphviz/information_content_entity_to_named_thing_association.gv b/graphviz/information_content_entity_to_named_thing_association.gv index fbf8324310..b788465b3b 100644 --- a/graphviz/information_content_entity_to_named_thing_association.gv +++ b/graphviz/information_content_entity_to_named_thing_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3016,283"]; + graph [bb="0,0,4748,283"]; node [label="\N"]; "information content entity to named thing association" [height=0.5, label="information content entity to named thing association", - pos="1551.4,265", + pos="2468.4,265", width=7.2577]; association [height=0.5, pos="62.394,178", width=1.7332]; "information content entity to named thing association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1291.1,263.37 974.46,261.47 458.75,254.41 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2208.4,263.14 1667.2,260.89 453.98,253.17 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "information content entity to named thing association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1295.4,261.29 1008.5,257.35 561.43,248.31 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2209.8,262.35 1692.6,258.65 565.38,248.46 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "information content entity to named thing association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1300.6,259.93 1042.6,254.96 658.37,245.16 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2210.5,261.98 1715.5,257.72 666.47,246.73 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "information content entity to named thing association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1298.8,260.4 1064.2,256.01 732.48,246.86 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2209.5,262.49 1733.1,259.21 751.51,250 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "information content entity to named thing association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1295.6,261.33 1087.6,257.7 811.16,249.14 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2208.1,263.34 1751.5,261.5 840.67,254.64 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "information content entity to named thing association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1302.4,259.46 1132.6,254.9 923.54,246 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2208.3,263.03 1781.3,260.75 966.09,253.24 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "information content entity to named thing association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1312.1,257.73 1216.1,252.86 1104.6,244.24 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2207.3,264.18 1851.5,263.32 1233.2,257.56 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "information content entity to named thing association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1338.1,254.58 1270.7,249.41 1196.1,241.4 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2207.3,264.18 1881.4,263.17 1342.9,257.09 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "information content entity to named thing association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1381.3,251.28 1337.9,246.13 1291.6,238.96 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2207.2,264.04 1913,262.71 1453.7,256.12 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "information content entity to named thing association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1453.9,248.24 1429,243.13 1402.5,236.75 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2208.8,262.8 1952.2,260.25 1577.6,252.47 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "information content entity to named thing association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1505.9,247.23 1497.5,242.42 1489.4,236.41 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2219.1,259.56 1975.5,254.37 1632.6,244.46 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "information content entity to named thing association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.7,247.07 1591.6,241.44 1602.5,235.06 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2217.6,259.89 2005,255.23 1731.4,245.97 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "information content entity to named thing association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1735.1,252.16 1765.8,246.9 1796.9,239.47 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,\ -202.83 1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2236.8,256.66 2088.3,250.77 1921.1,241.45 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,8 +140,8 @@ digraph { width=1.5346]; "information content entity to named thing association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.15 1733.9,252.12 1878.7,242.59 2057.5,230.57 2061.4,229 2069.3,225.82 2084,213.68 2096.8,202.16", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2278.2,252.64 2210.8,246.96 2148.6,239.1 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -152,9 +150,8 @@ digraph { width=1.0652]; "information content entity to named thing association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1735.8,252.22 1764.8,250.43 1794.4,248.64 1822.4,247 1896.2,242.69 2084.2,251.96 2154.4,229 2166,225.21 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2272.3,253.08 2245.6,247.76 2224,240.07 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -163,9 +160,8 @@ digraph { width=1.5887]; "information content entity to named thing association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.48 1732.8,252.01 1762.8,250.21 1793.4,248.47 1822.4,247 1874.3,244.37 2241.1,248.02 2289.4,229 2297.1,225.96 2311.1,\ -213.96 2323.5,202.48", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2374.8,248.19 2356.1,243.12 2340.4,236.75 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -174,88 +170,204 @@ digraph { width=1.0652]; "information content entity to named thing association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.42 1731,251.88 1761.5,250.07 1792.8,248.36 1822.4,247 1856.7,245.43 2411,248.16 2439.4,229 2447.3,223.69 2452.4,214.87 \ -2455.6,206.1", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "information content entity to named thing association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2542.6,247.66 2553.4,242.93 2563.8,236.84 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "information content entity to named thing association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2636.9,251.21 2660.9,245.98 2684.7,238.8 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "information content entity to named thing association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.51 2652.8,252.23 2739,245.75 2827,237.33 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "information content entity to named thing association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2996.9,196.19 2651,252.09 2797.3,242.45 2978.7,230.28 2980.4,229 2987.7,223.49 2992,214.74 2994.6,206.09", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "information content entity to named thing association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.3,196.07 2652.1,252.17 2681.3,250.38 2711.2,248.6 2739.4,247 2779,244.76 3061.6,248.22 3096.4,229 3106.1,223.62 3113.8,214.24 \ +3119.4,205.05", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "information content entity to named thing association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.09 2648.4,251.95 2678.8,250.13 2710,248.4 2739.4,247 2770.1,245.54 3265.8,244.38 3292.4,229 3301.6,223.69 3308.4,214.45 \ +3313.3,205.35", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "information content entity to named thing association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.18 2646.9,251.83 2677.7,250 2709.5,248.3 2739.4,247 2780.4,245.21 3442.2,248.41 3478.4,229 3488.2,223.74 3495.8,214.39 \ +3501.5,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "information content entity to named thing association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.73 2645.8,251.78 2677,249.95 2709.1,248.25 2739.4,247 2789.1,244.94 3591.2,251.85 3635.4,229 3645.7,223.67 3653.9,213.98 \ +3659.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "information content entity to named thing association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.76 2645.5,251.73 2676.7,249.9 2709,248.21 2739.4,247 2768.4,245.84 3758.4,241.96 3784.4,229 3795.1,223.66 3803.8,213.83 \ +3810.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "information content entity to named thing association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.78 2644.7,251.71 2676.2,249.87 2708.8,248.19 2739.4,247 2773.1,245.69 3924.1,243.85 3954.4,229 3965.2,223.68 3974.1,\ +213.87 3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "information content entity to named thing association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2644.4,251.69 2676,249.84 2708.7,248.16 2739.4,247 2777.6,245.55 4082,247.57 4115.4,229 4124.9,223.74 4131.9,214.39 \ +4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "information content entity to named thing association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.2,195.5 1729.9,251.83 1760.7,250.01 1792.5,248.3 1822.4,247 1842.9,246.11 2545.1,243.66 2559.4,229 2565.6,222.65 2565.4,213.6 \ -2562.9,204.95", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2644.4,251.66 2676,249.81 2708.7,248.14 2739.4,247 2760.7,246.21 4258.4,243.09 4274.4,229 4280.8,223.32 4283.4,214.65 \ +4284.1,206.11", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "information content entity to named thing association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.83 1729.5,251.82 1760.5,249.99 1792.4,248.29 1822.4,247 1865.6,245.14 2561.7,246.23 2601.4,229 2613.8,223.63 2624.6,\ -213.53 2632.9,203.8", + lp="4377.9,221.5", + pos="e,4367.7,195.47 2644,251.67 2675.7,249.81 2708.5,248.14 2739.4,247 2783.3,245.38 4278,243.68 4319.4,229 4334.6,223.59 4349,212.83 \ +4360.1,202.68", style=solid]; subject [height=0.5, - pos="2764.4,178", + pos="4496.4,178", width=1.2277]; "information content entity to named thing association" -> subject [color=blue, label=subject, - lp="2747.4,221.5", - pos="e,2747.4,194.72 1729.2,251.78 1760.2,249.95 1792.3,248.26 1822.4,247 1870.6,244.99 2644.4,243.6 2690.4,229 2708.4,223.29 2726,211.7 \ -2739.5,201.12", + lp="4473.4,221.5", + pos="e,4477.7,194.32 2644,251.65 2675.7,249.8 2708.5,248.13 2739.4,247 2832.3,243.59 4323.9,254.39 4413.4,229 4433.6,223.28 4453.7,211.29 \ +4469.2,200.49", style=solid]; object [height=0.5, - pos="2807.4,91", + pos="4539.4,91", width=1.0832]; "information content entity to named thing association" -> object [color=blue, label=object, - lp="2850.4,178", - pos="e,2820.8,108.09 1728.8,251.75 1760,249.92 1792.1,248.23 1822.4,247 1875.4,244.84 2727.6,247.41 2777.4,229 2819.9,213.29 2825.1,186.96 \ -2830.4,142 2831.2,135.38 2832.3,133.39 2830.4,127 2829.4,123.55 2827.9,120.13 2826.1,116.85", + lp="4583.4,178", + pos="e,4552.8,108.09 2644,251.64 2675.7,249.79 2708.5,248.12 2739.4,247 2788.4,245.22 4456.8,244.24 4503.4,229 4527.3,221.17 4535.3,216.87 \ +4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,116.85", style=solid]; predicate [height=0.5, - pos="2961.4,178", + pos="4693.4,178", width=1.5165]; "information content entity to named thing association" -> predicate [color=blue, label=predicate, - lp="2934.4,221.5", - pos="e,2937.6,194.29 1728.5,251.74 1759.7,249.9 1792,248.22 1822.4,247 1937.4,242.39 2746.4,255.77 2858.4,229 2883.3,223.06 2909.1,210.46 \ -2928.7,199.4", + lp="4666.4,221.5", + pos="e,4669.6,194.35 2643.6,251.65 2675.5,249.79 2708.4,248.12 2739.4,247 2842.2,243.28 4490.3,252.53 4590.4,229 4615.3,223.15 4641.2,\ +210.56 4660.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1869.4,265", + pos="2786.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2000.4,265", + pos="2917.4,265", width=2.0762]; subject -> object [label=relation, - lp="2802.4,134.5", - pos="e,2789.5,107.23 2765.5,159.55 2766.7,149.57 2769.2,137.07 2774.4,127 2776.6,122.68 2779.5,118.52 2782.7,114.66"]; + lp="4534.4,134.5", + pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; relation [height=0.5, - pos="2752.4,18", + pos="4484.4,18", width=1.2999]; - subject -> relation [pos="e,2753.7,36.188 2763.1,159.79 2761,132.48 2757,78.994 2754.5,46.38", + subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", style=dotted]; "information content entity to named thing association_subject" [color=blue, height=0.5, label="named thing", - pos="2162.4,265", + pos="3079.4,265", width=1.9318]; - object -> relation [pos="e,2765.2,35.54 2794.9,73.889 2788,64.939 2779.2,53.617 2771.4,43.584", + object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", style=dotted]; "information content entity to named thing association_object" [color=blue, height=0.5, label="named thing", - pos="2319.4,265", + pos="3236.4,265", width=1.9318]; "information content entity to named thing association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2485.4,265", + pos="3402.4,265", width=2.1665]; } diff --git a/graphviz/information_content_entity_to_named_thing_association.svg b/graphviz/information_content_entity_to_named_thing_association.svg index 521c1f6036..706430d3ea 100644 --- a/graphviz/information_content_entity_to_named_thing_association.svg +++ b/graphviz/information_content_entity_to_named_thing_association.svg @@ -4,16 +4,16 @@ - + %3 - + information content entity to named thing association - -information content entity to named thing association + +information content entity to named thing association @@ -24,9 +24,9 @@ information content entity to named thing association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ information content entity to named thing association->id - - -id + + +id @@ -50,9 +50,9 @@ information content entity to named thing association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ information content entity to named thing association->name - - -name + + +name @@ -76,9 +76,9 @@ information content entity to named thing association->description - - -description + + +description @@ -89,9 +89,9 @@ information content entity to named thing association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ information content entity to named thing association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ information content entity to named thing association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ information content entity to named thing association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ information content entity to named thing association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ information content entity to named thing association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ information content entity to named thing association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ information content entity to named thing association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ information content entity to named thing association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ information content entity to named thing association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ information content entity to named thing association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ information content entity to named thing association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +information content entity to named thing association->subject category + + +subject category + + + +object category + +ontology class + + + +information content entity to named thing association->object category + + +object category + + + +subject closure + +string + + + +information content entity to named thing association->subject closure + + +subject closure + + + +object closure + +string + + + +information content entity to named thing association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +information content entity to named thing association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +information content entity to named thing association->object category closure + + +object category closure + + + +subject namespace + +string + + + +information content entity to named thing association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +information content entity to named thing association->object namespace + + +object namespace + + + +subject label closure + +string + + + +information content entity to named thing association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +information content entity to named thing association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +information content entity to named thing association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + information content entity to named thing association->type - - -type + + +type - + category - -category + +category - + information content entity to named thing association->category - - -category + + +category - + subject - -subject + +subject - + information content entity to named thing association->subject - - -subject + + +subject - + object - -object + +object - + information content entity to named thing association->object - - -object + + +object - + predicate - -predicate + +predicate - + information content entity to named thing association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + information content entity to named thing association_subject - -named thing + +named thing - + object->relation - - + + - + information content entity to named thing association_object - -named thing + +named thing - + information content entity to named thing association_predicate - -predicate type + +predicate type diff --git a/graphviz/macromolecular_machine_to_biological_process_association.gv b/graphviz/macromolecular_machine_to_biological_process_association.gv index 91c51599be..92e16980d8 100644 --- a/graphviz/macromolecular_machine_to_biological_process_association.gv +++ b/graphviz/macromolecular_machine_to_biological_process_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3686.8,283"]; + graph [bb="0,0,5410.8,283"]; node [label="\N"]; "macromolecular machine to biological process association" [height=0.5, label="macromolecular machine to biological process association", - pos="2063.8,265", + pos="3046.8,265", width=7.7813]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "macromolecular machine to biological process association" -> "functional association" [label=is_a, - lp="728.79,221.5", - pos="e,190.45,190.88 1793,260.35 1520.5,255.88 1088.3,246.63 714.79,229 500.3,218.88 446.35,218.28 232.79,196 222.29,194.9 211.3,193.59 \ + lp="727.79,221.5", + pos="e,190.45,190.88 2766.5,264.63 2328.4,264.53 1454.4,259.94 713.79,229 499.7,220.06 445.91,218.25 232.79,196 222.29,194.9 211.3,193.59 \ 200.41,192.19"]; "macromolecular machine to entity association mixin" [height=0.5, pos="494.79,178", width=7.023]; "macromolecular machine to biological process association" -> "macromolecular machine to entity association mixin" [label=uses, - lp="903.29,221.5", - pos="e,595.22,194.54 1784.8,263.32 1546.1,260.92 1193.4,253.05 886.79,229 791.55,221.53 683.94,207.39 605.59,196.05"]; + lp="901.29,221.5", + pos="e,592.66,194.62 2767.6,263.35 2268.5,261.54 1242.1,254.72 884.79,229 789.17,222.12 681.08,207.74 602.99,196.16"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "macromolecular machine to biological process association" -> id [color=blue, label=id, - lp="1025.8,221.5", - pos="e,832.51,189.94 1794.9,259.93 1536.1,255.11 1163.2,245.58 1018.8,229 943.63,220.37 924.75,216.02 851.79,196 848.64,195.13 845.39,\ -194.16 842.15,193.14", + lp="1020.8,221.5", + pos="e,832.77,190 2770.3,262.06 2254.7,258.04 1183.3,247.56 1013.8,229 940.75,221 922.59,215.65 851.79,196 848.68,195.14 845.48,194.17 \ +842.28,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "macromolecular machine to biological process association" -> iri [color=blue, label=iri, - lp="1147.8,221.5", - pos="e,937.39,190.2 1784.3,263.68 1600.6,260.95 1355.3,252.5 1139.8,229 1058.1,220.09 1037.5,215.93 957.79,196 954.36,195.14 950.82,194.18 \ -947.29,193.17", + lp="1137.8,221.5", + pos="e,937.69,190.23 2766.5,264.78 2313.1,265.05 1438.2,261.16 1129.8,229 1052.4,220.93 1033.2,215.26 957.79,196 954.41,195.14 950.93,\ +194.18 947.45,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "macromolecular machine to biological process association" -> name [color=blue, label=name, - lp="1255.8,221.5", - pos="e,1063.6,190.89 1804.7,258.13 1603.6,252.62 1341.7,243.09 1235.8,229 1179.4,221.5 1116.1,205.55 1073.4,193.67", + lp="1249.8,221.5", + pos="e,1062.8,191.26 2770.8,261.91 2300,257.86 1377.9,247.67 1229.8,229 1175.1,222.11 1114,206.19 1072.6,194.15", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "macromolecular machine to biological process association" -> description [color=blue, label=description, - lp="1380.3,221.5", - pos="e,1212.4,193.56 1804.6,258.12 1633.9,252.96 1426.4,243.9 1339.8,229 1299.3,222.04 1254.9,208.3 1222.1,196.99", + lp="1378.3,221.5", + pos="e,1211.2,193.64 2769.3,262.49 2321.3,259.43 1474.6,250.83 1337.8,229 1297.4,222.56 1253.2,208.65 1220.8,197.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "macromolecular machine to biological process association" -> "has attribute" [color=blue, label="has attribute", - lp="1531.8,221.5", - pos="e,1352.6,191.7 1792,260.58 1694.5,255.93 1584.2,246.72 1484.8,229 1442.4,221.43 1395.5,206.69 1362.4,195.16", + lp="1535.8,221.5", + pos="e,1352.4,191.74 2770.9,261.74 2357.2,257.76 1611.3,248.05 1488.8,229 1444.7,222.14 1395.9,206.98 1362,195.14", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "macromolecular machine to biological process association" -> predicate [color=blue, label=predicate, - lp="1681.8,221.5", - pos="e,1509.4,193.2 1848,253.49 1783.3,248.28 1712.4,240.53 1647.8,229 1603.8,221.14 1555,207.36 1519.2,196.25", + lp="1695.8,221.5", + pos="e,1510,193.08 2766.8,264.38 2425.1,263.53 1867.3,257.58 1661.8,229 1613,222.22 1558.9,207.75 1520,196.12", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "macromolecular machine to biological process association" -> negated [color=blue, label=negated, - lp="1803.8,221.5", - pos="e,1645,189.93 1907.8,250.05 1864.5,244.84 1817.6,237.94 1774.8,229 1724.8,218.56 1713.6,210.87 1664.8,196 1661.5,194.99 1658.1,193.95 \ -1654.6,192.9", + lp="1840.8,221.5", + pos="e,1644.4,190.21 2769.6,262.34 2463.4,259.41 1990,251.31 1811.8,229 1756.5,222.07 1694.5,205.34 1653.9,193.13", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "macromolecular machine to biological process association" -> qualifiers [color=blue, label=qualifiers, - lp="1912.3,221.5", - pos="e,1784.7,194.24 1961.7,248.19 1934.5,243.03 1905.3,236.63 1878.8,229 1849.9,220.71 1818.5,208.5 1794.1,198.21", + lp="1976.3,221.5", + pos="e,1793.3,193 2769.8,262.26 2495.9,259.26 2096.2,251.12 1942.8,229 1894.8,222.07 1841.4,207.62 1803.2,196.03", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "macromolecular machine to biological process association" -> publications [color=blue, label=publications, - lp="2015.8,221.5", - pos="e,1925.8,195.45 2011.5,247.2 1998.2,242.09 1984.1,235.97 1971.8,229 1958.3,221.42 1944.7,211.19 1933.5,201.95", + lp="2116.8,221.5", + pos="e,1943.5,192.76 2770.5,262 2530.6,258.8 2201.9,250.51 2072.8,229 2031.5,222.11 1986,207.8 1953.3,196.25", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "macromolecular machine to biological process association" -> "has evidence" [color=blue, label="has evidence", - lp="2110.3,221.5", - pos="e,2063.8,196.18 2063.8,246.8 2063.8,235.16 2063.8,219.55 2063.8,206.24", + lp="2268.3,221.5", + pos="e,2100.8,193.77 2776.5,260.2 2577.6,255.96 2324.6,247.12 2221.8,229 2183.4,222.24 2141.5,208.65 2110.4,197.35", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "macromolecular machine to biological process association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2258.3,221.5", - pos="e,2233.5,195.37 2113.5,247.12 2128.8,241.65 2145.6,235.34 2160.8,229 2182.1,220.11 2205.3,209.19 2224.5,199.83", + lp="2414.3,221.5", + pos="e,2287.2,195.77 2767.1,263.58 2608.2,260.67 2426.1,252.07 2349.8,229 2330.5,223.17 2311,212 2295.7,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "macromolecular machine to biological process association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2480.8,221.5", - pos="e,2454.4,194.37 2203,249.37 2243.1,244.1 2286.9,237.34 2326.8,229 2366.7,220.66 2410.8,207.94 2444.7,197.41", + lp="2581.8,221.5", + pos="e,2488.6,196.25 2802.5,256.18 2656.9,250.28 2498.2,241.12 2486.8,229 2480.8,222.6 2481.4,213.84 2484.4,205.44", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,8 +147,8 @@ digraph { width=3.015]; "macromolecular machine to biological process association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2743.3,221.5", - pos="e,2695.8,194.8 2257.4,251.96 2397,243.1 2563.6,232.09 2579.8,229 2616.2,222.03 2656,209.19 2686.3,198.27", + lp="2790.3,221.5", + pos="e,2701.7,195.1 2822,254.18 2754.2,248.9 2694.6,240.92 2683.8,229 2675,219.36 2682,209.3 2693.3,200.75", style=solid]; timepoint [color=blue, height=0.5, @@ -158,9 +157,8 @@ digraph { width=1.5346]; "macromolecular machine to biological process association" -> timepoint [color=blue, label=timepoint, - lp="2916.8,221.5", - pos="e,2902.7,195.34 2257.7,251.98 2289.5,250.19 2322,248.46 2352.8,247 2408.4,244.36 2801.5,248.08 2853.8,229 2869.3,223.35 2884,212.42 \ -2895.4,202.22", + lp="2939.8,221.5", + pos="e,2906.7,195.8 2945.5,248.17 2926.7,243.17 2910.9,236.84 2904.8,229 2899.5,222.2 2900,213.44 2902.7,205.16", style=solid]; "original subject" [color=blue, height=0.5, @@ -169,9 +167,8 @@ digraph { width=1.0652]; "macromolecular machine to biological process association" -> "original subject" [color=blue, label="original subject", - lp="3042.8,221.5", - pos="e,3013.1,194.43 2256.1,251.91 2288.4,250.1 2321.5,248.39 2352.8,247 2419.8,244.03 2892,249.58 2955.8,229 2973.9,223.17 2991.6,211.46 \ -3005.2,200.84", + lp="3036.8,221.5", + pos="e,3003.7,191.31 2999.3,247.11 2991.9,242.39 2985.3,236.45 2980.8,229 2973.5,216.95 2982.8,205.59 2995.2,196.74", style=solid]; "original predicate" [color=blue, height=0.5, @@ -180,85 +177,201 @@ digraph { width=1.5887]; "macromolecular machine to biological process association" -> "original predicate" [color=blue, label="original predicate", - lp="3184.3,221.5", - pos="e,3134.9,196.25 2255,251.82 2287.6,250 2321.2,248.31 2352.8,247 2394.4,245.28 3065.3,247.28 3102.8,229 3113.6,223.72 3122.5,214.1 \ -3129.3,204.69", + lp="3172.3,221.5", + pos="e,3127.7,195.75 3070.6,246.75 3077.9,241.26 3085.8,235.04 3092.8,229 3102.2,220.85 3112.1,211.38 3120.6,202.9", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3275.8,178", + pos="3257.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "original object" [color=blue, label="original object", - lp="3316.3,221.5", - pos="e,3272.5,196 2253.8,251.77 2286.8,249.95 2320.8,248.26 2352.8,247 2377.7,246.02 3230.8,242.51 3251.8,229 3260.1,223.64 3265.6,214.53 \ -3269.2,205.53", + lp="3302.3,221.5", + pos="e,3255.9,196.32 3182.3,249.21 3207.8,244.18 3229.7,237.58 3239.8,229 3246.6,223.24 3250.8,214.7 3253.5,206.3", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3390.8,178", + width=2.1304]; + "macromolecular machine to biological process association" -> "subject category" [color=blue, + label="subject category", + lp="3433.3,221.5", + pos="e,3384,196.3 3259.4,253.22 3301.9,248.03 3339.3,240.36 3357.8,229 3366.9,223.43 3374,214.32 3379.2,205.38", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3561.8,178", + width=2.1304]; + "macromolecular machine to biological process association" -> "object category" [color=blue, + label="object category", + lp="3578.3,221.5", + pos="e,3545.6,195.85 3236.2,251.72 3353.5,243.71 3484.1,233.86 3496.8,229 3512,223.15 3526.6,212.53 3538.1,202.57", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3694.8,178", + width=1.0652]; + "macromolecular machine to biological process association" -> "subject closure" [color=blue, + label="subject closure", + lp="3715.3,221.5", + pos="e,3681.7,195.2 3245.5,252.28 3417,242.15 3637.5,229.12 3637.8,229 3651.8,223.26 3664.7,212.62 3674.6,202.63", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3794.8,178", + width=1.0652]; + "macromolecular machine to biological process association" -> "object closure" [color=blue, + label="object closure", + lp="3835.8,221.5", + pos="e,3792.3,196.35 3241.9,252.05 3273.3,250.27 3305.4,248.52 3335.8,247 3360.1,245.78 3753.8,242.89 3773.8,229 3781.5,223.61 3786.4,\ +214.78 3789.5,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3927.8,178", + width=2.1304]; + "macromolecular machine to biological process association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3994.3,221.5", + pos="e,3919.8,196.18 3239.9,251.93 3271.9,250.14 3304.8,248.42 3335.8,247 3366.6,245.6 3862.4,243.13 3889.8,229 3900.1,223.69 3908.4,\ +214.2 3914.5,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4119.8,178", + width=2.1304]; + "macromolecular machine to biological process association" -> "object category closure" [color=blue, + label="object category closure", + lp="4185.3,221.5", + pos="e,4113.1,196.16 3238,251.82 3270.6,250 3304.2,248.31 3335.8,247 3377.4,245.28 4049.2,248.94 4085.8,229 4095.5,223.73 4102.9,214.37 \ +4108.4,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4309.8,178", + width=1.0652]; + "macromolecular machine to biological process association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4357.8,221.5", + pos="e,4302.4,195.73 3236.8,251.75 3269.8,249.93 3303.8,248.25 3335.8,247 3387.8,244.97 4226.5,252.88 4272.8,229 4283.1,223.67 4291.3,\ +213.99 4297.3,204.55", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4468.8,178", + width=1.0652]; + "macromolecular machine to biological process association" -> "object namespace" [color=blue, + label="object namespace", + lp="4511.8,221.5", + pos="e,4460.8,195.77 3236,251.72 3269.2,249.89 3303.5,248.21 3335.8,247 3366.2,245.86 4402.6,242.56 4429.8,229 4440.5,223.66 4449.1,213.84 \ +4455.6,204.3", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4619.8,178", + width=1.0652]; + "macromolecular machine to biological process association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4671.8,221.5", + pos="e,4611.5,195.79 3235.6,251.69 3269,249.85 3303.4,248.19 3335.8,247 3370.3,245.73 4548.8,244.2 4579.8,229 4590.6,223.69 4599.5,213.87 \ +4606.1,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4790.8,178", + width=1.0652]; + "macromolecular machine to biological process association" -> "object label closure" [color=blue, + label="object label closure", + lp="4839.3,221.5", + pos="e,4782.2,195.8 3235.2,251.66 3268.7,249.83 3303.3,248.16 3335.8,247 3375,245.6 4714.4,246.03 4749.8,229 4760.8,223.71 4769.8,213.89 \ +4776.6,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4952.8,178", + width=2.347]; + "macromolecular machine to biological process association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5001.3,221.5", + pos="e,4944.2,196.29 3234.8,251.65 3268.4,249.81 3303.1,248.15 3335.8,247 3379.6,245.46 4873.4,248.2 4912.8,229 4923.5,223.78 4932.3,\ +214.16 4938.8,204.75", style=solid]; type [height=0.5, - pos="3363.8,178", + pos="5086.8,178", width=0.86659]; "macromolecular machine to biological process association" -> type [color=blue, label=type, - lp="3393.8,221.5", - pos="e,3372.7,195.56 2253.4,251.73 2286.5,249.91 2320.6,248.23 2352.8,247 2381.1,245.92 3351.9,249.19 3371.8,229 3377.9,222.78 3378.1,\ -213.87 3376,205.3", + lp="5100.8,221.5", + pos="e,5087.6,196.18 3234.8,251.62 3268.4,249.78 3303.1,248.13 3335.8,247 3359.9,246.17 5055.9,244.05 5074.8,229 5081.6,223.54 5085,214.92 \ +5086.5,206.37", style=solid]; category [height=0.5, - pos="3464.8,178", + pos="5187.8,178", width=1.4263]; "macromolecular machine to biological process association" -> category [color=blue, label=category, - lp="3468.3,221.5", - pos="e,3453.1,195.87 2253.4,251.71 2286.5,249.89 2320.6,248.22 2352.8,247 2411.7,244.77 3359.4,251.75 3413.8,229 3426.6,223.64 3438,213.39 \ -3446.7,203.56", + lp="5181.3,221.5", + pos="e,5172.2,195.25 3234.4,251.63 3268.2,249.79 3303,248.13 3335.8,247 3385.3,245.29 5073.8,244.86 5120.8,229 5137,223.53 5152.5,212.51 \ +5164.5,202.2", style=solid]; subject [height=0.5, - pos="3578.8,178", + pos="5301.8,178", width=1.2277]; "macromolecular machine to biological process association" -> subject [color=blue, label=subject, - lp="3561.8,221.5", - pos="e,3561.5,194.76 2253,251.7 2286.2,249.87 2320.5,248.2 2352.8,247 2416.7,244.62 3442.7,248.01 3503.8,229 3522,223.34 3539.8,211.75 \ -3553.5,201.16", + lp="5277.8,221.5", + pos="e,5282.5,194.33 3234.4,251.62 3268.2,249.77 3303,248.12 3335.8,247 3388,245.22 5166.4,242.97 5216.8,229 5237.5,223.25 5258.4,211.08 \ +5274.3,200.2", style=solid]; object [height=0.5, - pos="3621.8,91", + pos="5344.8,91", width=1.0832]; "macromolecular machine to biological process association" -> object [color=blue, label=object, - lp="3664.8,178", - pos="e,3635.2,108.09 2252.6,251.69 2286,249.86 2320.4,248.19 2352.8,247 2421.6,244.48 3527.2,252.75 3591.8,229 3634.3,213.38 3639.5,186.96 \ -3644.8,142 3645.6,135.38 3646.7,133.39 3644.8,127 3643.8,123.55 3642.3,120.13 3640.5,116.85", + lp="5388.8,178", + pos="e,5358.2,108.09 3234.4,251.6 3268.2,249.76 3303,248.11 3335.8,247 3390.5,245.14 5255.6,245.74 5307.8,229 5332.1,221.2 5340.4,217.1 \ +5354.8,196 5368.7,175.59 5364.9,166.51 5367.8,142 5368.6,135.38 5369.7,133.39 5367.8,127 5366.8,123.55 5365.3,120.13 5363.5,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2399.8,265", + pos="3382.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2530.8,265", + pos="3513.8,265", width=2.0762]; subject -> object [label=relation, - lp="3616.8,134.5", - pos="e,3603.9,107.23 3579.9,159.55 3581.1,149.57 3583.6,137.07 3588.8,127 3591,122.68 3593.9,118.52 3597.1,114.66"]; + lp="5339.8,134.5", + pos="e,5326.9,107.23 5302.9,159.55 5304.1,149.57 5306.6,137.07 5311.8,127 5314,122.68 5316.9,118.52 5320.1,114.66"]; relation [height=0.5, - pos="3566.8,18", + pos="5289.8,18", width=1.2999]; - subject -> relation [pos="e,3568.1,36.188 3577.5,159.79 3575.4,132.48 3571.3,78.994 3568.9,46.38", + subject -> relation [pos="e,5291.1,36.188 5300.5,159.79 5298.4,132.48 5294.3,78.994 5291.9,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="2779.8,265", + pos="3762.8,265", width=4.3329]; - object -> relation [pos="e,3579.6,35.54 3609.3,73.889 3602.4,64.939 3593.6,53.617 3585.8,43.584", + object -> relation [pos="e,5302.6,35.54 5332.3,73.889 5325.4,64.939 5316.6,53.617 5308.8,43.584", style=dotted]; "macromolecular machine to biological process association_object" [color=blue, height=0.5, label="biological process", - pos="3047.8,265", + pos="4030.8,265", width=2.5998]; } diff --git a/graphviz/macromolecular_machine_to_biological_process_association.svg b/graphviz/macromolecular_machine_to_biological_process_association.svg index ecc4f4dbfc..68c94bf9e0 100644 --- a/graphviz/macromolecular_machine_to_biological_process_association.svg +++ b/graphviz/macromolecular_machine_to_biological_process_association.svg @@ -4,16 +4,16 @@ - + %3 - + macromolecular machine to biological process association - -macromolecular machine to biological process association + +macromolecular machine to biological process association @@ -24,9 +24,9 @@ macromolecular machine to biological process association->functional association - + -is_a +is_a @@ -37,9 +37,9 @@ macromolecular machine to biological process association->macromolecular machine to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ macromolecular machine to biological process association->id - - -id + + +id @@ -63,9 +63,9 @@ macromolecular machine to biological process association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ macromolecular machine to biological process association->name - - -name + + +name @@ -89,9 +89,9 @@ macromolecular machine to biological process association->description - - -description + + +description @@ -102,9 +102,9 @@ macromolecular machine to biological process association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ macromolecular machine to biological process association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ macromolecular machine to biological process association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ macromolecular machine to biological process association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ macromolecular machine to biological process association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ macromolecular machine to biological process association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ macromolecular machine to biological process association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ macromolecular machine to biological process association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ macromolecular machine to biological process association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ macromolecular machine to biological process association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ macromolecular machine to biological process association->original subject - - -original subject + + +original subject @@ -245,123 +245,266 @@ macromolecular machine to biological process association->original predicate - - -original predicate + + +original predicate original object - -string + +string macromolecular machine to biological process association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +macromolecular machine to biological process association->subject category + + +subject category + + + +object category + +ontology class + + + +macromolecular machine to biological process association->object category + + +object category + + + +subject closure + +string + + + +macromolecular machine to biological process association->subject closure + + +subject closure + + + +object closure + +string + + + +macromolecular machine to biological process association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +macromolecular machine to biological process association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +macromolecular machine to biological process association->object category closure + + +object category closure + + + +subject namespace + +string + + + +macromolecular machine to biological process association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +macromolecular machine to biological process association->object namespace + + +object namespace + + + +subject label closure + +string + + + +macromolecular machine to biological process association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +macromolecular machine to biological process association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +macromolecular machine to biological process association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + macromolecular machine to biological process association->type - - -type + + +type - + category - -category + +category - + macromolecular machine to biological process association->category - - -category + + +category - + subject - -subject + +subject - + macromolecular machine to biological process association->subject - - -subject + + +subject - + object - -object + +object - + macromolecular machine to biological process association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin - + object->relation - - + + - + macromolecular machine to biological process association_object - -biological process + +biological process diff --git a/graphviz/macromolecular_machine_to_cellular_component_association.gv b/graphviz/macromolecular_machine_to_cellular_component_association.gv index dc853f682c..4b555d2197 100644 --- a/graphviz/macromolecular_machine_to_cellular_component_association.gv +++ b/graphviz/macromolecular_machine_to_cellular_component_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3686.8,283"]; + graph [bb="0,0,5410.8,283"]; node [label="\N"]; "macromolecular machine to cellular component association" [height=0.5, label="macromolecular machine to cellular component association", - pos="2063.8,265", + pos="3046.8,265", width=7.9437]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "macromolecular machine to cellular component association" -> "functional association" [label=is_a, - lp="728.79,221.5", - pos="e,190.45,190.88 1787.9,260.26 1515.1,255.76 1086,246.52 714.79,229 500.3,218.88 446.35,218.28 232.79,196 222.29,194.9 211.3,193.59 \ + lp="727.79,221.5", + pos="e,190.45,190.88 2760.7,264.63 2320.6,264.49 1451.2,259.8 713.79,229 499.7,220.06 445.91,218.25 232.79,196 222.29,194.9 211.3,193.59 \ 200.41,192.19"]; "macromolecular machine to entity association mixin" [height=0.5, pos="494.79,178", width=7.023]; "macromolecular machine to cellular component association" -> "macromolecular machine to entity association mixin" [label=uses, - lp="903.29,221.5", - pos="e,595.22,194.54 1778.9,263.26 1540.2,260.79 1190.8,252.85 886.79,229 791.55,221.53 683.94,207.39 605.59,196.05"]; + lp="901.29,221.5", + pos="e,592.66,194.62 2761.7,263.33 2260.5,261.49 1240.7,254.62 884.79,229 789.17,222.12 681.08,207.74 602.99,196.16"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "macromolecular machine to cellular component association" -> id [color=blue, label=id, - lp="1025.8,221.5", - pos="e,832.51,189.94 1789.8,259.83 1531.1,254.99 1162.3,245.47 1018.8,229 943.63,220.37 924.75,216.02 851.79,196 848.64,195.13 845.39,\ -194.16 842.15,193.14", + lp="1020.8,221.5", + pos="e,832.77,190 2764.5,262.02 2246.7,257.96 1182.6,247.49 1013.8,229 940.75,221 922.59,215.65 851.79,196 848.68,195.14 845.48,194.17 \ +842.28,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "macromolecular machine to cellular component association" -> iri [color=blue, label=iri, - lp="1147.8,221.5", - pos="e,937.39,190.2 1778.7,263.6 1595.6,260.78 1353.1,252.26 1139.8,229 1058.1,220.09 1037.5,215.93 957.79,196 954.36,195.14 950.82,194.18 \ -947.29,193.17", + lp="1137.8,221.5", + pos="e,937.69,190.23 2760.6,264.78 2305.5,265.01 1436.9,261.02 1129.8,229 1052.4,220.93 1033.2,215.26 957.79,196 954.41,195.14 950.93,\ +194.18 947.45,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "macromolecular machine to cellular component association" -> name [color=blue, label=name, - lp="1255.8,221.5", - pos="e,1063.6,190.89 1800.1,258 1599.6,252.47 1340.9,242.99 1235.8,229 1179.4,221.5 1116.1,205.55 1073.4,193.67", + lp="1249.8,221.5", + pos="e,1062.8,191.26 2764.7,261.86 2292.1,257.77 1377.3,247.59 1229.8,229 1175.1,222.11 1114,206.19 1072.6,194.15", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "macromolecular machine to cellular component association" -> description [color=blue, label=description, - lp="1380.3,221.5", - pos="e,1212.4,193.56 1800.1,257.98 1630.2,252.8 1425.6,243.77 1339.8,229 1299.3,222.04 1254.9,208.3 1222.1,196.99", + lp="1378.3,221.5", + pos="e,1211.2,193.64 2763.4,262.45 2313.9,259.36 1474,250.73 1337.8,229 1297.4,222.56 1253.2,208.65 1220.8,197.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "macromolecular machine to cellular component association" -> "has attribute" [color=blue, label="has attribute", - lp="1531.8,221.5", - pos="e,1352.6,191.7 1787.2,260.35 1690.9,255.63 1582.6,246.44 1484.8,229 1442.4,221.43 1395.5,206.69 1362.4,195.16", + lp="1535.8,221.5", + pos="e,1352.4,191.74 2765.4,261.69 2350.6,257.68 1610.8,247.97 1488.8,229 1444.7,222.14 1395.9,206.98 1362,195.14", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "macromolecular machine to cellular component association" -> predicate [color=blue, label=predicate, - lp="1681.8,221.5", - pos="e,1509.4,193.2 1845.8,253.31 1781.7,248.11 1711.6,240.4 1647.8,229 1603.8,221.14 1555,207.36 1519.2,196.25", + lp="1695.8,221.5", + pos="e,1510,193.08 2760.9,264.36 2418.6,263.46 1866.2,257.41 1661.8,229 1613,222.22 1558.9,207.75 1520,196.12", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "macromolecular machine to cellular component association" -> negated [color=blue, label=negated, - lp="1803.8,221.5", - pos="e,1645,189.93 1906.6,249.91 1863.6,244.72 1817.2,237.86 1774.8,229 1724.8,218.56 1713.6,210.87 1664.8,196 1661.5,194.99 1658.1,193.95 \ -1654.6,192.9", + lp="1840.8,221.5", + pos="e,1644.4,190.21 2763.8,262.29 2457.4,259.31 1988.8,251.17 1811.8,229 1756.5,222.07 1694.5,205.34 1653.9,193.13", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "macromolecular machine to cellular component association" -> qualifiers [color=blue, label=qualifiers, - lp="1912.3,221.5", - pos="e,1784.7,194.24 1961.2,248.1 1934.2,242.95 1905.2,236.58 1878.8,229 1849.9,220.71 1818.5,208.5 1794.1,198.21", + lp="1976.3,221.5", + pos="e,1793.3,193 2764.1,262.19 2490.4,259.15 2095.1,250.97 1942.8,229 1894.8,222.07 1841.4,207.62 1803.2,196.03", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "macromolecular machine to cellular component association" -> publications [color=blue, label=publications, - lp="2015.8,221.5", - pos="e,1925.8,195.45 2011.5,247.2 1998.2,242.09 1984.1,235.97 1971.8,229 1958.3,221.42 1944.7,211.19 1933.5,201.95", + lp="2116.8,221.5", + pos="e,1943.5,192.76 2765,261.92 2525.6,258.67 2200.9,250.34 2072.8,229 2031.5,222.11 1986,207.8 1953.3,196.25", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "macromolecular machine to cellular component association" -> "has evidence" [color=blue, label="has evidence", - lp="2110.3,221.5", - pos="e,2063.8,196.18 2063.8,246.8 2063.8,235.16 2063.8,219.55 2063.8,206.24", + lp="2268.3,221.5", + pos="e,2100.8,193.77 2771.4,260.09 2573.3,255.8 2323.8,246.97 2221.8,229 2183.4,222.24 2141.5,208.65 2110.4,197.35", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "macromolecular machine to cellular component association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2258.3,221.5", - pos="e,2233.5,195.37 2113.5,247.12 2128.8,241.65 2145.6,235.34 2160.8,229 2182.1,220.11 2205.3,209.19 2224.5,199.83", + lp="2414.3,221.5", + pos="e,2287.2,195.77 2761.7,263.48 2604.1,260.47 2425.2,251.81 2349.8,229 2330.5,223.17 2311,212 2295.7,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "macromolecular machine to cellular component association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2480.8,221.5", - pos="e,2454.4,194.37 2203.7,249.28 2243.6,244.02 2287.1,237.29 2326.8,229 2366.7,220.66 2410.8,207.94 2444.7,197.41", + lp="2581.8,221.5", + pos="e,2488.6,196.25 2798.5,256.01 2654,250.11 2498.1,241.01 2486.8,229 2480.8,222.6 2481.4,213.84 2484.4,205.44", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,8 +147,8 @@ digraph { width=3.015]; "macromolecular machine to cellular component association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2743.3,221.5", - pos="e,2695.8,194.8 2269.1,252.44 2399.4,244.69 2549.1,234.87 2579.8,229 2616.2,222.03 2656,209.19 2686.3,198.27", + lp="2790.3,221.5", + pos="e,2701.7,195.1 2820,254.02 2753,248.74 2694.5,240.8 2683.8,229 2675,219.36 2682,209.3 2693.3,200.75", style=solid]; timepoint [color=blue, height=0.5, @@ -158,9 +157,8 @@ digraph { width=1.5346]; "macromolecular machine to cellular component association" -> timepoint [color=blue, label=timepoint, - lp="2916.8,221.5", - pos="e,2902.7,195.34 2262.1,251.99 2294.4,250.2 2327.5,248.47 2358.8,247 2413.8,244.42 2802.1,247.86 2853.8,229 2869.3,223.35 2884,212.42 \ -2895.4,202.21", + lp="2939.8,221.5", + pos="e,2906.7,195.8 2945.2,248.07 2926.5,243.09 2910.9,236.79 2904.8,229 2899.5,222.2 2900,213.44 2902.7,205.16", style=solid]; "original subject" [color=blue, height=0.5, @@ -169,9 +167,8 @@ digraph { width=1.0652]; "macromolecular machine to cellular component association" -> "original subject" [color=blue, label="original subject", - lp="3042.8,221.5", - pos="e,3013.1,194.43 2260.5,251.91 2293.3,250.11 2327,248.39 2358.8,247 2425.1,244.09 2892.6,249.38 2955.8,229 2973.9,223.16 2991.6,211.46 \ -3005.2,200.83", + lp="3036.8,221.5", + pos="e,3003.7,191.31 2999.3,247.11 2991.9,242.39 2985.3,236.45 2980.8,229 2973.5,216.95 2982.8,205.59 2995.2,196.74", style=solid]; "original predicate" [color=blue, height=0.5, @@ -180,85 +177,202 @@ digraph { width=1.5887]; "macromolecular machine to cellular component association" -> "original predicate" [color=blue, label="original predicate", - lp="3184.3,221.5", - pos="e,3134.9,196.25 2258.9,251.83 2292.2,250.02 2326.5,248.32 2358.8,247 2400.1,245.31 3065.6,247.14 3102.8,229 3113.6,223.72 3122.5,\ -214.1 3129.3,204.69", + lp="3172.3,221.5", + pos="e,3127.7,195.75 3070.6,246.75 3077.9,241.26 3085.8,235.04 3092.8,229 3102.2,220.85 3112.1,211.38 3120.6,202.9", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3275.8,178", + pos="3257.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "original object" [color=blue, label="original object", - lp="3316.3,221.5", - pos="e,3272.5,196 2258.1,251.77 2291.7,249.95 2326.2,248.27 2358.8,247 2383.6,246.04 3230.9,242.42 3251.8,229 3260.1,223.64 3265.6,214.52 \ -3269.2,205.53", + lp="3302.3,221.5", + pos="e,3255.9,196.32 3182.7,249.11 3208.1,244.1 3229.7,237.52 3239.8,229 3246.6,223.24 3250.8,214.7 3253.5,206.3", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3390.8,178", + width=2.1304]; + "macromolecular machine to cellular component association" -> "subject category" [color=blue, + label="subject category", + lp="3433.3,221.5", + pos="e,3384,196.3 3261,253.02 3302.9,247.84 3339.5,240.21 3357.8,229 3366.9,223.43 3374,214.32 3379.2,205.38", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3561.8,178", + width=2.1304]; + "macromolecular machine to cellular component association" -> "object category" [color=blue, + label="object category", + lp="3578.3,221.5", + pos="e,3545.6,195.85 3238.1,251.59 3354.9,243.6 3484.2,233.84 3496.8,229 3512,223.15 3526.6,212.53 3538.1,202.57", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3694.8,178", + width=1.0652]; + "macromolecular machine to cellular component association" -> "subject closure" [color=blue, + label="subject closure", + lp="3715.3,221.5", + pos="e,3681.7,195.2 3248.8,252.22 3419.5,242.24 3636.6,229.47 3637.8,229 3651.8,223.26 3664.7,212.62 3674.6,202.63", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3794.8,178", + width=1.0652]; + "macromolecular machine to cellular component association" -> "object closure" [color=blue, + label="object closure", + lp="3835.8,221.5", + pos="e,3792.3,196.35 3246.3,252.07 3278.2,250.29 3310.9,248.53 3341.8,247 3365.8,245.81 3754.1,242.71 3773.8,229 3781.5,223.61 3786.4,\ +214.77 3789.5,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3927.8,178", + width=2.1304]; + "macromolecular machine to cellular component association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3994.3,221.5", + pos="e,3919.8,196.18 3244.3,251.94 3276.9,250.15 3310.3,248.43 3341.8,247 3372.2,245.62 3862.7,242.98 3889.8,229 3900.1,223.69 3908.4,\ +214.19 3914.5,204.89", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4119.8,178", + width=2.1304]; + "macromolecular machine to cellular component association" -> "object category closure" [color=blue, + label="object category closure", + lp="4185.3,221.5", + pos="e,4113.1,196.16 3241.9,251.83 3275.2,250.02 3309.5,248.32 3341.8,247 3383.1,245.31 4049.5,248.78 4085.8,229 4095.5,223.73 4102.9,\ +214.37 4108.4,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4309.8,178", + width=1.0652]; + "macromolecular machine to cellular component association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4357.8,221.5", + pos="e,4302.4,195.73 3240.7,251.76 3274.4,249.94 3309.1,248.26 3341.8,247 3393.5,245.01 4226.8,252.73 4272.8,229 4283.1,223.67 4291.3,\ +213.99 4297.3,204.55", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4468.8,178", + width=1.0652]; + "macromolecular machine to cellular component association" -> "object namespace" [color=blue, + label="object namespace", + lp="4511.8,221.5", + pos="e,4460.8,195.77 3240.3,251.71 3274.1,249.89 3309,248.22 3341.8,247 3372,245.88 4402.7,242.49 4429.8,229 4440.5,223.66 4449.1,213.84 \ +4455.6,204.3", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4619.8,178", + width=1.0652]; + "macromolecular machine to cellular component association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4671.8,221.5", + pos="e,4611.5,195.79 3239.5,251.7 3273.6,249.86 3308.7,248.19 3341.8,247 3376.2,245.76 4548.9,244.12 4579.8,229 4590.6,223.69 4599.5,\ +213.87 4606.1,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4790.8,178", + width=1.0652]; + "macromolecular machine to cellular component association" -> "object label closure" [color=blue, + label="object label closure", + lp="4839.3,221.5", + pos="e,4782.2,195.8 3239.1,251.67 3273.3,249.83 3308.6,248.17 3341.8,247 3380.9,245.62 4714.5,245.96 4749.8,229 4760.8,223.71 4769.8,\ +213.89 4776.6,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4952.8,178", + width=2.347]; + "macromolecular machine to cellular component association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5001.3,221.5", + pos="e,4944.2,196.29 3238.7,251.65 3273,249.81 3308.5,248.15 3341.8,247 3385.4,245.49 4873.6,248.13 4912.8,229 4923.5,223.78 4932.3,214.16 \ +4938.8,204.75", style=solid]; type [height=0.5, - pos="3363.8,178", + pos="5086.8,178", width=0.86659]; "macromolecular machine to cellular component association" -> type [color=blue, label=type, - lp="3393.8,221.5", - pos="e,3372.7,195.56 2257.3,251.74 2291.1,249.92 2326,248.24 2358.8,247 2386.9,245.94 3352.1,249.08 3371.8,229 3377.9,222.78 3378.1,213.87 \ -3376,205.3", + lp="5100.8,221.5", + pos="e,5087.6,196.18 3238.7,251.62 3273,249.79 3308.5,248.13 3341.8,247 3365.8,246.18 5056,244 5074.8,229 5081.6,223.54 5085,214.92 5086.5,\ +206.37", style=solid]; category [height=0.5, - pos="3464.8,178", + pos="5187.8,178", width=1.4263]; "macromolecular machine to cellular component association" -> category [color=blue, label=category, - lp="3468.3,221.5", - pos="e,3453.1,195.87 2257.3,251.72 2291.1,249.9 2326,248.22 2358.8,247 2417.4,244.81 3359.7,251.63 3413.8,229 3426.6,223.64 3438,213.39 \ -3446.7,203.56", + lp="5181.3,221.5", + pos="e,5172.2,195.25 3238.7,251.62 3273,249.78 3308.5,248.13 3341.8,247 3391.2,245.33 5074,244.81 5120.8,229 5137,223.53 5152.5,212.51 \ +5164.5,202.2", style=solid]; subject [height=0.5, - pos="3578.8,178", + pos="5301.8,178", width=1.2277]; "macromolecular machine to cellular component association" -> subject [color=blue, label=subject, - lp="3561.8,221.5", - pos="e,3561.5,194.75 2256.9,251.71 2290.9,249.88 2325.9,248.21 2358.8,247 2422.4,244.67 3443,247.91 3503.8,229 3522,223.34 3539.8,211.75 \ -3553.5,201.16", + lp="5277.8,221.5", + pos="e,5282.5,194.33 3238.3,251.62 3272.8,249.78 3308.3,248.12 3341.8,247 3393.8,245.25 5166.6,242.93 5216.8,229 5237.5,223.25 5258.4,\ +211.08 5274.3,200.2", style=solid]; object [height=0.5, - pos="3621.8,91", + pos="5344.8,91", width=1.0832]; "macromolecular machine to cellular component association" -> object [color=blue, label=object, - lp="3664.8,178", - pos="e,3635.2,108.09 2256.5,251.7 2290.6,249.86 2325.7,248.19 2358.8,247 2427.3,244.53 3527.5,252.63 3591.8,229 3634.3,213.38 3639.5,\ -186.96 3644.8,142 3645.6,135.38 3646.7,133.39 3644.8,127 3643.8,123.55 3642.3,120.13 3640.5,116.85", + lp="5388.8,178", + pos="e,5358.2,108.09 3238.3,251.61 3272.8,249.77 3308.3,248.12 3341.8,247 3396.4,245.18 5255.8,245.69 5307.8,229 5332.1,221.2 5340.4,\ +217.1 5354.8,196 5368.7,175.59 5364.9,166.51 5367.8,142 5368.6,135.38 5369.7,133.39 5367.8,127 5366.8,123.55 5365.3,120.13 5363.5,\ +116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2405.8,265", + pos="3388.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2536.8,265", + pos="3519.8,265", width=2.0762]; subject -> object [label=relation, - lp="3616.8,134.5", - pos="e,3603.9,107.23 3579.9,159.55 3581.1,149.57 3583.6,137.07 3588.8,127 3591,122.68 3593.9,118.52 3597.1,114.66"]; + lp="5339.8,134.5", + pos="e,5326.9,107.23 5302.9,159.55 5304.1,149.57 5306.6,137.07 5311.8,127 5314,122.68 5316.9,118.52 5320.1,114.66"]; relation [height=0.5, - pos="3566.8,18", + pos="5289.8,18", width=1.2999]; - subject -> relation [pos="e,3568.1,36.188 3577.5,159.79 3575.4,132.48 3571.3,78.994 3568.9,46.38", + subject -> relation [pos="e,5291.1,36.188 5300.5,159.79 5298.4,132.48 5294.3,78.994 5291.9,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="2785.8,265", + pos="3768.8,265", width=4.3329]; - object -> relation [pos="e,3579.6,35.54 3609.3,73.889 3602.4,64.939 3593.6,53.617 3585.8,43.584", + object -> relation [pos="e,5302.6,35.54 5332.3,73.889 5325.4,64.939 5316.6,53.617 5308.8,43.584", style=dotted]; "macromolecular machine to cellular component association_object" [color=blue, height=0.5, label="cellular component", - pos="3058.8,265", + pos="4041.8,265", width=2.7623]; } diff --git a/graphviz/macromolecular_machine_to_cellular_component_association.svg b/graphviz/macromolecular_machine_to_cellular_component_association.svg index db56ca8e4d..dad3abac52 100644 --- a/graphviz/macromolecular_machine_to_cellular_component_association.svg +++ b/graphviz/macromolecular_machine_to_cellular_component_association.svg @@ -4,16 +4,16 @@ - + %3 - + macromolecular machine to cellular component association - -macromolecular machine to cellular component association + +macromolecular machine to cellular component association @@ -24,9 +24,9 @@ macromolecular machine to cellular component association->functional association - + -is_a +is_a @@ -37,9 +37,9 @@ macromolecular machine to cellular component association->macromolecular machine to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ macromolecular machine to cellular component association->id - - -id + + +id @@ -63,9 +63,9 @@ macromolecular machine to cellular component association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ macromolecular machine to cellular component association->name - - -name + + +name @@ -89,9 +89,9 @@ macromolecular machine to cellular component association->description - - -description + + +description @@ -102,9 +102,9 @@ macromolecular machine to cellular component association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ macromolecular machine to cellular component association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ macromolecular machine to cellular component association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ macromolecular machine to cellular component association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ macromolecular machine to cellular component association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ macromolecular machine to cellular component association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ macromolecular machine to cellular component association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ macromolecular machine to cellular component association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ macromolecular machine to cellular component association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ macromolecular machine to cellular component association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ macromolecular machine to cellular component association->original subject - - -original subject + + +original subject @@ -245,123 +245,266 @@ macromolecular machine to cellular component association->original predicate - - -original predicate + + +original predicate original object - -string + +string macromolecular machine to cellular component association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +macromolecular machine to cellular component association->subject category + + +subject category + + + +object category + +ontology class + + + +macromolecular machine to cellular component association->object category + + +object category + + + +subject closure + +string + + + +macromolecular machine to cellular component association->subject closure + + +subject closure + + + +object closure + +string + + + +macromolecular machine to cellular component association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +macromolecular machine to cellular component association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +macromolecular machine to cellular component association->object category closure + + +object category closure + + + +subject namespace + +string + + + +macromolecular machine to cellular component association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +macromolecular machine to cellular component association->object namespace + + +object namespace + + + +subject label closure + +string + + + +macromolecular machine to cellular component association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +macromolecular machine to cellular component association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +macromolecular machine to cellular component association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + macromolecular machine to cellular component association->type - - -type + + +type - + category - -category + +category - + macromolecular machine to cellular component association->category - - -category + + +category - + subject - -subject + +subject - + macromolecular machine to cellular component association->subject - - -subject + + +subject - + object - -object + +object - + macromolecular machine to cellular component association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin - + object->relation - - + + - + macromolecular machine to cellular component association_object - -cellular component + +cellular component diff --git a/graphviz/macromolecular_machine_to_molecular_activity_association.gv b/graphviz/macromolecular_machine_to_molecular_activity_association.gv index 0f0b016653..39f48f525d 100644 --- a/graphviz/macromolecular_machine_to_molecular_activity_association.gv +++ b/graphviz/macromolecular_machine_to_molecular_activity_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3686.8,283"]; + graph [bb="0,0,5410.8,283"]; node [label="\N"]; "macromolecular machine to molecular activity association" [height=0.5, label="macromolecular machine to molecular activity association", - pos="2063.8,265", + pos="3046.8,265", width=7.7813]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "macromolecular machine to molecular activity association" -> "functional association" [label=is_a, - lp="728.79,221.5", - pos="e,190.45,190.88 1793,260.35 1520.5,255.88 1088.3,246.63 714.79,229 500.3,218.88 446.35,218.28 232.79,196 222.29,194.9 211.3,193.59 \ + lp="727.79,221.5", + pos="e,190.45,190.88 2766.5,264.63 2328.4,264.53 1454.4,259.94 713.79,229 499.7,220.06 445.91,218.25 232.79,196 222.29,194.9 211.3,193.59 \ 200.41,192.19"]; "macromolecular machine to entity association mixin" [height=0.5, pos="494.79,178", width=7.023]; "macromolecular machine to molecular activity association" -> "macromolecular machine to entity association mixin" [label=uses, - lp="903.29,221.5", - pos="e,595.22,194.54 1784.8,263.32 1546.1,260.92 1193.4,253.05 886.79,229 791.55,221.53 683.94,207.39 605.59,196.05"]; + lp="901.29,221.5", + pos="e,592.66,194.62 2767.6,263.35 2268.5,261.54 1242.1,254.72 884.79,229 789.17,222.12 681.08,207.74 602.99,196.16"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "macromolecular machine to molecular activity association" -> id [color=blue, label=id, - lp="1025.8,221.5", - pos="e,832.51,189.94 1794.9,259.93 1536.1,255.11 1163.2,245.58 1018.8,229 943.63,220.37 924.75,216.02 851.79,196 848.64,195.13 845.39,\ -194.16 842.15,193.14", + lp="1020.8,221.5", + pos="e,832.77,190 2770.3,262.06 2254.7,258.04 1183.3,247.56 1013.8,229 940.75,221 922.59,215.65 851.79,196 848.68,195.14 845.48,194.17 \ +842.28,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "macromolecular machine to molecular activity association" -> iri [color=blue, label=iri, - lp="1147.8,221.5", - pos="e,937.39,190.2 1784.3,263.68 1600.6,260.95 1355.3,252.5 1139.8,229 1058.1,220.09 1037.5,215.93 957.79,196 954.36,195.14 950.82,194.18 \ -947.29,193.17", + lp="1137.8,221.5", + pos="e,937.69,190.23 2766.5,264.78 2313.1,265.05 1438.2,261.16 1129.8,229 1052.4,220.93 1033.2,215.26 957.79,196 954.41,195.14 950.93,\ +194.18 947.45,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "macromolecular machine to molecular activity association" -> name [color=blue, label=name, - lp="1255.8,221.5", - pos="e,1063.6,190.89 1804.7,258.13 1603.6,252.62 1341.7,243.09 1235.8,229 1179.4,221.5 1116.1,205.55 1073.4,193.67", + lp="1249.8,221.5", + pos="e,1062.8,191.26 2770.8,261.91 2300,257.86 1377.9,247.67 1229.8,229 1175.1,222.11 1114,206.19 1072.6,194.15", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "macromolecular machine to molecular activity association" -> description [color=blue, label=description, - lp="1380.3,221.5", - pos="e,1212.4,193.56 1804.6,258.12 1633.9,252.96 1426.4,243.9 1339.8,229 1299.3,222.04 1254.9,208.3 1222.1,196.99", + lp="1378.3,221.5", + pos="e,1211.2,193.64 2769.3,262.49 2321.3,259.43 1474.6,250.83 1337.8,229 1297.4,222.56 1253.2,208.65 1220.8,197.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "macromolecular machine to molecular activity association" -> "has attribute" [color=blue, label="has attribute", - lp="1531.8,221.5", - pos="e,1352.6,191.7 1792,260.58 1694.5,255.93 1584.2,246.72 1484.8,229 1442.4,221.43 1395.5,206.69 1362.4,195.16", + lp="1535.8,221.5", + pos="e,1352.4,191.74 2770.9,261.74 2357.2,257.76 1611.3,248.05 1488.8,229 1444.7,222.14 1395.9,206.98 1362,195.14", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "macromolecular machine to molecular activity association" -> predicate [color=blue, label=predicate, - lp="1681.8,221.5", - pos="e,1509.4,193.2 1848,253.49 1783.3,248.28 1712.4,240.53 1647.8,229 1603.8,221.14 1555,207.36 1519.2,196.25", + lp="1695.8,221.5", + pos="e,1510,193.08 2766.8,264.38 2425.1,263.53 1867.3,257.58 1661.8,229 1613,222.22 1558.9,207.75 1520,196.12", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "macromolecular machine to molecular activity association" -> negated [color=blue, label=negated, - lp="1803.8,221.5", - pos="e,1645,189.93 1907.8,250.05 1864.5,244.84 1817.6,237.94 1774.8,229 1724.8,218.56 1713.6,210.87 1664.8,196 1661.5,194.99 1658.1,193.95 \ -1654.6,192.9", + lp="1840.8,221.5", + pos="e,1644.4,190.21 2769.6,262.34 2463.4,259.41 1990,251.31 1811.8,229 1756.5,222.07 1694.5,205.34 1653.9,193.13", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "macromolecular machine to molecular activity association" -> qualifiers [color=blue, label=qualifiers, - lp="1912.3,221.5", - pos="e,1784.7,194.24 1961.7,248.19 1934.5,243.03 1905.3,236.63 1878.8,229 1849.9,220.71 1818.5,208.5 1794.1,198.21", + lp="1976.3,221.5", + pos="e,1793.3,193 2769.8,262.26 2495.9,259.26 2096.2,251.12 1942.8,229 1894.8,222.07 1841.4,207.62 1803.2,196.03", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "macromolecular machine to molecular activity association" -> publications [color=blue, label=publications, - lp="2015.8,221.5", - pos="e,1925.8,195.45 2011.5,247.2 1998.2,242.09 1984.1,235.97 1971.8,229 1958.3,221.42 1944.7,211.19 1933.5,201.95", + lp="2116.8,221.5", + pos="e,1943.5,192.76 2770.5,262 2530.6,258.8 2201.9,250.51 2072.8,229 2031.5,222.11 1986,207.8 1953.3,196.25", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "macromolecular machine to molecular activity association" -> "has evidence" [color=blue, label="has evidence", - lp="2110.3,221.5", - pos="e,2063.8,196.18 2063.8,246.8 2063.8,235.16 2063.8,219.55 2063.8,206.24", + lp="2268.3,221.5", + pos="e,2100.8,193.77 2776.5,260.2 2577.6,255.96 2324.6,247.12 2221.8,229 2183.4,222.24 2141.5,208.65 2110.4,197.35", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "macromolecular machine to molecular activity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2258.3,221.5", - pos="e,2233.5,195.37 2113.5,247.12 2128.8,241.65 2145.6,235.34 2160.8,229 2182.1,220.11 2205.3,209.19 2224.5,199.83", + lp="2414.3,221.5", + pos="e,2287.2,195.77 2767.1,263.58 2608.2,260.67 2426.1,252.07 2349.8,229 2330.5,223.17 2311,212 2295.7,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "macromolecular machine to molecular activity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2480.8,221.5", - pos="e,2454.4,194.37 2203,249.37 2243.1,244.1 2286.9,237.34 2326.8,229 2366.7,220.66 2410.8,207.94 2444.7,197.41", + lp="2581.8,221.5", + pos="e,2488.6,196.25 2802.5,256.18 2656.9,250.28 2498.2,241.12 2486.8,229 2480.8,222.6 2481.4,213.84 2484.4,205.44", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,8 +147,8 @@ digraph { width=3.015]; "macromolecular machine to molecular activity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2743.3,221.5", - pos="e,2695.8,194.8 2257.4,251.96 2397,243.1 2563.6,232.09 2579.8,229 2616.2,222.03 2656,209.19 2686.3,198.27", + lp="2790.3,221.5", + pos="e,2701.7,195.1 2822,254.18 2754.2,248.9 2694.6,240.92 2683.8,229 2675,219.36 2682,209.3 2693.3,200.75", style=solid]; timepoint [color=blue, height=0.5, @@ -158,9 +157,8 @@ digraph { width=1.5346]; "macromolecular machine to molecular activity association" -> timepoint [color=blue, label=timepoint, - lp="2916.8,221.5", - pos="e,2902.7,195.34 2257.7,251.98 2289.5,250.19 2322,248.46 2352.8,247 2408.4,244.36 2801.5,248.08 2853.8,229 2869.3,223.35 2884,212.42 \ -2895.4,202.22", + lp="2939.8,221.5", + pos="e,2906.7,195.8 2945.5,248.17 2926.7,243.17 2910.9,236.84 2904.8,229 2899.5,222.2 2900,213.44 2902.7,205.16", style=solid]; "original subject" [color=blue, height=0.5, @@ -169,9 +167,8 @@ digraph { width=1.0652]; "macromolecular machine to molecular activity association" -> "original subject" [color=blue, label="original subject", - lp="3042.8,221.5", - pos="e,3013.1,194.43 2256.1,251.91 2288.4,250.1 2321.5,248.39 2352.8,247 2419.8,244.03 2892,249.58 2955.8,229 2973.9,223.17 2991.6,211.46 \ -3005.2,200.84", + lp="3036.8,221.5", + pos="e,3003.7,191.31 2999.3,247.11 2991.9,242.39 2985.3,236.45 2980.8,229 2973.5,216.95 2982.8,205.59 2995.2,196.74", style=solid]; "original predicate" [color=blue, height=0.5, @@ -180,85 +177,201 @@ digraph { width=1.5887]; "macromolecular machine to molecular activity association" -> "original predicate" [color=blue, label="original predicate", - lp="3184.3,221.5", - pos="e,3134.9,196.25 2255,251.82 2287.6,250 2321.2,248.31 2352.8,247 2394.4,245.28 3065.3,247.28 3102.8,229 3113.6,223.72 3122.5,214.1 \ -3129.3,204.69", + lp="3172.3,221.5", + pos="e,3127.7,195.75 3070.6,246.75 3077.9,241.26 3085.8,235.04 3092.8,229 3102.2,220.85 3112.1,211.38 3120.6,202.9", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3275.8,178", + pos="3257.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "original object" [color=blue, label="original object", - lp="3316.3,221.5", - pos="e,3272.5,196 2253.8,251.77 2286.8,249.95 2320.8,248.26 2352.8,247 2377.7,246.02 3230.8,242.51 3251.8,229 3260.1,223.64 3265.6,214.53 \ -3269.2,205.53", + lp="3302.3,221.5", + pos="e,3255.9,196.32 3182.3,249.21 3207.8,244.18 3229.7,237.58 3239.8,229 3246.6,223.24 3250.8,214.7 3253.5,206.3", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3390.8,178", + width=2.1304]; + "macromolecular machine to molecular activity association" -> "subject category" [color=blue, + label="subject category", + lp="3433.3,221.5", + pos="e,3384,196.3 3259.4,253.22 3301.9,248.03 3339.3,240.36 3357.8,229 3366.9,223.43 3374,214.32 3379.2,205.38", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3561.8,178", + width=2.1304]; + "macromolecular machine to molecular activity association" -> "object category" [color=blue, + label="object category", + lp="3578.3,221.5", + pos="e,3545.6,195.85 3236.2,251.72 3353.5,243.71 3484.1,233.86 3496.8,229 3512,223.15 3526.6,212.53 3538.1,202.57", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3694.8,178", + width=1.0652]; + "macromolecular machine to molecular activity association" -> "subject closure" [color=blue, + label="subject closure", + lp="3715.3,221.5", + pos="e,3681.7,195.2 3245.5,252.28 3417,242.15 3637.5,229.12 3637.8,229 3651.8,223.26 3664.7,212.62 3674.6,202.63", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3794.8,178", + width=1.0652]; + "macromolecular machine to molecular activity association" -> "object closure" [color=blue, + label="object closure", + lp="3835.8,221.5", + pos="e,3792.3,196.35 3241.9,252.05 3273.3,250.27 3305.4,248.52 3335.8,247 3360.1,245.78 3753.8,242.89 3773.8,229 3781.5,223.61 3786.4,\ +214.78 3789.5,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3927.8,178", + width=2.1304]; + "macromolecular machine to molecular activity association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3994.3,221.5", + pos="e,3919.8,196.18 3239.9,251.93 3271.9,250.14 3304.8,248.42 3335.8,247 3366.6,245.6 3862.4,243.13 3889.8,229 3900.1,223.69 3908.4,\ +214.2 3914.5,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4119.8,178", + width=2.1304]; + "macromolecular machine to molecular activity association" -> "object category closure" [color=blue, + label="object category closure", + lp="4185.3,221.5", + pos="e,4113.1,196.16 3238,251.82 3270.6,250 3304.2,248.31 3335.8,247 3377.4,245.28 4049.2,248.94 4085.8,229 4095.5,223.73 4102.9,214.37 \ +4108.4,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4309.8,178", + width=1.0652]; + "macromolecular machine to molecular activity association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4357.8,221.5", + pos="e,4302.4,195.73 3236.8,251.75 3269.8,249.93 3303.8,248.25 3335.8,247 3387.8,244.97 4226.5,252.88 4272.8,229 4283.1,223.67 4291.3,\ +213.99 4297.3,204.55", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4468.8,178", + width=1.0652]; + "macromolecular machine to molecular activity association" -> "object namespace" [color=blue, + label="object namespace", + lp="4511.8,221.5", + pos="e,4460.8,195.77 3236,251.72 3269.2,249.89 3303.5,248.21 3335.8,247 3366.2,245.86 4402.6,242.56 4429.8,229 4440.5,223.66 4449.1,213.84 \ +4455.6,204.3", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4619.8,178", + width=1.0652]; + "macromolecular machine to molecular activity association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4671.8,221.5", + pos="e,4611.5,195.79 3235.6,251.69 3269,249.85 3303.4,248.19 3335.8,247 3370.3,245.73 4548.8,244.2 4579.8,229 4590.6,223.69 4599.5,213.87 \ +4606.1,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4790.8,178", + width=1.0652]; + "macromolecular machine to molecular activity association" -> "object label closure" [color=blue, + label="object label closure", + lp="4839.3,221.5", + pos="e,4782.2,195.8 3235.2,251.66 3268.7,249.83 3303.3,248.16 3335.8,247 3375,245.6 4714.4,246.03 4749.8,229 4760.8,223.71 4769.8,213.89 \ +4776.6,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4952.8,178", + width=2.347]; + "macromolecular machine to molecular activity association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5001.3,221.5", + pos="e,4944.2,196.29 3234.8,251.65 3268.4,249.81 3303.1,248.15 3335.8,247 3379.6,245.46 4873.4,248.2 4912.8,229 4923.5,223.78 4932.3,\ +214.16 4938.8,204.75", style=solid]; type [height=0.5, - pos="3363.8,178", + pos="5086.8,178", width=0.86659]; "macromolecular machine to molecular activity association" -> type [color=blue, label=type, - lp="3393.8,221.5", - pos="e,3372.7,195.56 2253.4,251.73 2286.5,249.91 2320.6,248.23 2352.8,247 2381.1,245.92 3351.9,249.19 3371.8,229 3377.9,222.78 3378.1,\ -213.87 3376,205.3", + lp="5100.8,221.5", + pos="e,5087.6,196.18 3234.8,251.62 3268.4,249.78 3303.1,248.13 3335.8,247 3359.9,246.17 5055.9,244.05 5074.8,229 5081.6,223.54 5085,214.92 \ +5086.5,206.37", style=solid]; category [height=0.5, - pos="3464.8,178", + pos="5187.8,178", width=1.4263]; "macromolecular machine to molecular activity association" -> category [color=blue, label=category, - lp="3468.3,221.5", - pos="e,3453.1,195.87 2253.4,251.71 2286.5,249.89 2320.6,248.22 2352.8,247 2411.7,244.77 3359.4,251.75 3413.8,229 3426.6,223.64 3438,213.39 \ -3446.7,203.56", + lp="5181.3,221.5", + pos="e,5172.2,195.25 3234.4,251.63 3268.2,249.79 3303,248.13 3335.8,247 3385.3,245.29 5073.8,244.86 5120.8,229 5137,223.53 5152.5,212.51 \ +5164.5,202.2", style=solid]; subject [height=0.5, - pos="3578.8,178", + pos="5301.8,178", width=1.2277]; "macromolecular machine to molecular activity association" -> subject [color=blue, label=subject, - lp="3561.8,221.5", - pos="e,3561.5,194.76 2253,251.7 2286.2,249.87 2320.5,248.2 2352.8,247 2416.7,244.62 3442.7,248.01 3503.8,229 3522,223.34 3539.8,211.75 \ -3553.5,201.16", + lp="5277.8,221.5", + pos="e,5282.5,194.33 3234.4,251.62 3268.2,249.77 3303,248.12 3335.8,247 3388,245.22 5166.4,242.97 5216.8,229 5237.5,223.25 5258.4,211.08 \ +5274.3,200.2", style=solid]; object [height=0.5, - pos="3621.8,91", + pos="5344.8,91", width=1.0832]; "macromolecular machine to molecular activity association" -> object [color=blue, label=object, - lp="3664.8,178", - pos="e,3635.2,108.09 2252.6,251.69 2286,249.86 2320.4,248.19 2352.8,247 2421.6,244.48 3527.2,252.75 3591.8,229 3634.3,213.38 3639.5,186.96 \ -3644.8,142 3645.6,135.38 3646.7,133.39 3644.8,127 3643.8,123.55 3642.3,120.13 3640.5,116.85", + lp="5388.8,178", + pos="e,5358.2,108.09 3234.4,251.6 3268.2,249.76 3303,248.11 3335.8,247 3390.5,245.14 5255.6,245.74 5307.8,229 5332.1,221.2 5340.4,217.1 \ +5354.8,196 5368.7,175.59 5364.9,166.51 5367.8,142 5368.6,135.38 5369.7,133.39 5367.8,127 5366.8,123.55 5365.3,120.13 5363.5,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2399.8,265", + pos="3382.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2530.8,265", + pos="3513.8,265", width=2.0762]; subject -> object [label=relation, - lp="3616.8,134.5", - pos="e,3603.9,107.23 3579.9,159.55 3581.1,149.57 3583.6,137.07 3588.8,127 3591,122.68 3593.9,118.52 3597.1,114.66"]; + lp="5339.8,134.5", + pos="e,5326.9,107.23 5302.9,159.55 5304.1,149.57 5306.6,137.07 5311.8,127 5314,122.68 5316.9,118.52 5320.1,114.66"]; relation [height=0.5, - pos="3566.8,18", + pos="5289.8,18", width=1.2999]; - subject -> relation [pos="e,3568.1,36.188 3577.5,159.79 3575.4,132.48 3571.3,78.994 3568.9,46.38", + subject -> relation [pos="e,5291.1,36.188 5300.5,159.79 5298.4,132.48 5294.3,78.994 5291.9,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="2779.8,265", + pos="3762.8,265", width=4.3329]; - object -> relation [pos="e,3579.6,35.54 3609.3,73.889 3602.4,64.939 3593.6,53.617 3585.8,43.584", + object -> relation [pos="e,5302.6,35.54 5332.3,73.889 5325.4,64.939 5316.6,53.617 5308.8,43.584", style=dotted]; "macromolecular machine to molecular activity association_object" [color=blue, height=0.5, label="molecular activity", - pos="3047.8,265", + pos="4030.8,265", width=2.6178]; } diff --git a/graphviz/macromolecular_machine_to_molecular_activity_association.svg b/graphviz/macromolecular_machine_to_molecular_activity_association.svg index 0fce88a769..8193592edc 100644 --- a/graphviz/macromolecular_machine_to_molecular_activity_association.svg +++ b/graphviz/macromolecular_machine_to_molecular_activity_association.svg @@ -4,16 +4,16 @@ - + %3 - + macromolecular machine to molecular activity association - -macromolecular machine to molecular activity association + +macromolecular machine to molecular activity association @@ -24,9 +24,9 @@ macromolecular machine to molecular activity association->functional association - + -is_a +is_a @@ -37,9 +37,9 @@ macromolecular machine to molecular activity association->macromolecular machine to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ macromolecular machine to molecular activity association->id - - -id + + +id @@ -63,9 +63,9 @@ macromolecular machine to molecular activity association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ macromolecular machine to molecular activity association->name - - -name + + +name @@ -89,9 +89,9 @@ macromolecular machine to molecular activity association->description - - -description + + +description @@ -102,9 +102,9 @@ macromolecular machine to molecular activity association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ macromolecular machine to molecular activity association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ macromolecular machine to molecular activity association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ macromolecular machine to molecular activity association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ macromolecular machine to molecular activity association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ macromolecular machine to molecular activity association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ macromolecular machine to molecular activity association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ macromolecular machine to molecular activity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ macromolecular machine to molecular activity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ macromolecular machine to molecular activity association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ macromolecular machine to molecular activity association->original subject - - -original subject + + +original subject @@ -245,123 +245,266 @@ macromolecular machine to molecular activity association->original predicate - - -original predicate + + +original predicate original object - -string + +string macromolecular machine to molecular activity association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +macromolecular machine to molecular activity association->subject category + + +subject category + + + +object category + +ontology class + + + +macromolecular machine to molecular activity association->object category + + +object category + + + +subject closure + +string + + + +macromolecular machine to molecular activity association->subject closure + + +subject closure + + + +object closure + +string + + + +macromolecular machine to molecular activity association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +macromolecular machine to molecular activity association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +macromolecular machine to molecular activity association->object category closure + + +object category closure + + + +subject namespace + +string + + + +macromolecular machine to molecular activity association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +macromolecular machine to molecular activity association->object namespace + + +object namespace + + + +subject label closure + +string + + + +macromolecular machine to molecular activity association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +macromolecular machine to molecular activity association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +macromolecular machine to molecular activity association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + macromolecular machine to molecular activity association->type - - -type + + +type - + category - -category + +category - + macromolecular machine to molecular activity association->category - - -category + + +category - + subject - -subject + +subject - + macromolecular machine to molecular activity association->subject - - -subject + + +subject - + object - -object + +object - + macromolecular machine to molecular activity association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin - + object->relation - - + + - + macromolecular machine to molecular activity association_object - -molecular activity + +molecular activity diff --git a/graphviz/material_sample_derivation_association.gv b/graphviz/material_sample_derivation_association.gv index 7c6110a622..6ea69c3f36 100644 --- a/graphviz/material_sample_derivation_association.gv +++ b/graphviz/material_sample_derivation_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3016,283"]; + graph [bb="0,0,4748,283"]; node [label="\N"]; "material sample derivation association" [height=0.5, label="material sample derivation association", - pos="1551.4,265", + pos="2468.4,265", width=5.2898]; association [height=0.5, pos="62.394,178", width=1.7332]; "material sample derivation association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1361.2,263.73 1056.8,262.46 473.59,256.39 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2278.4,263.42 1780.4,261.56 462.57,254.27 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "material sample derivation association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1363.2,262.16 1084.5,258.78 575.35,249.91 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2279.1,262.83 1801.8,259.59 573.73,249.38 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "material sample derivation association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1365.4,261.13 1111.9,256.63 671.27,246.58 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2279.3,262.56 1820.8,258.78 674.59,247.61 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "material sample derivation association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1364.3,261.55 1130.9,257.72 745.07,248.6 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2279.1,262.95 1836.5,260.13 759.52,251.08 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "material sample derivation association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1362.9,262.38 1151.8,259.48 823.51,251.4 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2278.5,263.59 1852.9,262.2 848.53,256.04 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "material sample derivation association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1365.3,261.01 1188.2,257.05 934.57,248.18 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2278.4,263.38 1878.2,261.56 973.67,254.64 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "material sample derivation association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1367.6,260.21 1261,256.04 1124.6,247.28 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2278.1,264.3 1940.3,264.02 1248.9,259.56 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "material sample derivation association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1378.5,257.42 1301.5,252.51 1209.9,243.94 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2277.9,264.33 1965.6,263.97 1358,259.23 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "material sample derivation association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1402.7,253.7 1353.5,248.45 1298.7,240.63 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2278,264.27 1992.8,263.67 1468.2,258.42 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "material sample derivation association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1458.8,249.24 1432.5,243.98 1404.1,237.26 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2278.6,263.4 2025.5,261.59 1591.3,254.7 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "material sample derivation association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1506.2,247.43 1497.7,242.58 1489.5,236.51 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2282.9,260.86 2040.3,256.12 1638.2,245.86 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "material sample derivation association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.7,247.07 1591.6,241.44 1602.5,235.06 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2282.1,261.2 2065.1,257.08 1733.4,247.75 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "material sample derivation association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1687.1,252.35 1742.6,246.41 1799.7,238.44 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,\ -202.83 1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2290,258.65 2131.4,253 1922.5,242.96 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "material sample derivation association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.18 1685,252.14 1707.2,250.32 1729.9,248.54 1751.4,247 1820.2,242.08 1997.2,254.36 2061.4,229 2069.3,225.86 2084,213.72 \ -2096.8,202.19", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2308.9,255.07 2230.8,249.28 2150.4,240.63 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "material sample derivation association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1683.4,252.02 1706.1,250.18 1729.4,248.43 1751.4,247 1840.9,241.2 2069.1,256.46 2154.4,229 2166,225.26 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2296.8,257.15 2259.2,251.96 2226.9,243.3 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "material sample derivation association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.49 1682.3,251.9 1705.3,250.05 1729,248.32 1751.4,247 1811.1,243.47 2233.7,250.77 2289.4,229 2297.1,225.98 2311.2,213.98 \ -2323.5,202.49", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2378.3,249.11 2358.1,243.89 2340.8,237.23 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "material sample derivation association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.43 1681.5,251.83 1704.8,249.97 1728.8,248.26 1751.4,247 1789.6,244.88 2407.6,250.31 2439.4,229 2447.3,223.7 2452.4,\ -214.88 2455.6,206.11", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "material sample derivation association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2541,248.35 2552.4,243.53 2563.4,237.23 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "material sample derivation association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2621.8,254.26 2650.7,248.88 2680.1,240.87 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "material sample derivation association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.51 2604.6,252.39 2710.2,243.21 2839.8,231.55 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "material sample derivation association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2996.9,196.22 2602,252.13 2624.2,250.31 2646.9,248.53 2668.4,247 2703,244.53 2952.6,249.78 2980.4,229 2987.7,223.52 2992.1,214.79 \ +2994.7,206.14", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "material sample derivation association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.11 2600.1,252 2622.9,250.15 2646.3,248.4 2668.4,247 2715.9,243.98 3054.6,251.86 3096.4,229 3106.2,223.66 3113.8,214.28 \ +3119.4,205.09", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "material sample derivation association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.1 2598.8,251.86 2621.9,250 2645.9,248.28 2668.4,247 2703,245.03 3262.3,246.3 3292.4,229 3301.6,223.71 3308.4,214.47 \ +3313.3,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "material sample derivation association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.19 2598,251.8 2621.4,249.93 2645.6,248.22 2668.4,247 2713.3,244.59 3438.7,250.23 3478.4,229 3488.2,223.75 3495.9,214.4 \ +3501.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "material sample derivation association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.73 2597.7,251.75 2621.2,249.88 2645.5,248.18 2668.4,247 2722.1,244.22 3587.6,253.63 3635.4,229 3645.7,223.67 3653.9,213.99 \ +3659.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "material sample derivation association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.77 2597.4,251.72 2621,249.85 2645.4,248.16 2668.4,247 2699.4,245.44 3756.6,242.83 3784.4,229 3795.1,223.66 3803.8,213.84 \ +3810.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "material sample derivation association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2597.1,251.71 2620.8,249.83 2645.3,248.14 2668.4,247 2704.1,245.24 3922.3,244.7 3954.4,229 3965.3,223.69 3974.1,\ +213.87 3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "material sample derivation association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2596.9,251.7 2620.6,249.81 2645.2,248.13 2668.4,247 2708.5,245.05 4080.3,248.52 4115.4,229 4124.9,223.75 4131.9,\ +214.39 4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "material sample derivation association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.3,195.51 1681,251.8 1704.4,249.93 1728.6,248.22 1751.4,247 1773.8,245.8 2543.7,245.05 2559.4,229 2565.6,222.65 2565.4,213.61 \ -2562.9,204.95", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2596.9,251.67 2620.6,249.79 2645.2,248.11 2668.4,247 2690.7,245.93 4257.6,243.73 4274.4,229 4280.9,223.32 4283.4,\ +214.65 4284.1,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "material sample derivation association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.84 1681,251.78 1704.4,249.91 1728.6,248.21 1751.4,247 1798.6,244.5 2558,247.76 2601.4,229 2613.8,223.65 2624.6,213.54 \ -2632.9,203.81", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2596.6,251.69 2620.4,249.8 2645.2,248.11 2668.4,247 2714.2,244.81 4276.2,244.33 4319.4,229 4334.6,223.59 4349,212.83 \ +4360.1,202.68", style=solid]; subject [height=0.5, - pos="2764.4,178", + pos="4496.4,178", width=1.2277]; "material sample derivation association" -> subject [color=blue, label=subject, - lp="2747.4,221.5", - pos="e,2747.4,194.73 1680.7,251.76 1704.2,249.89 1728.5,248.19 1751.4,247 1803.5,244.29 2640.7,244.75 2690.4,229 2708.4,223.3 2726,211.72 \ -2739.5,201.13", + lp="4473.4,221.5", + pos="e,4477.7,194.32 2596.6,251.68 2620.4,249.79 2645.2,248.11 2668.4,247 2765.2,242.39 4320.1,255.44 4413.4,229 4433.6,223.29 4453.7,\ +211.3 4469.2,200.49", style=solid]; object [height=0.5, - pos="2807.4,91", + pos="4539.4,91", width=1.0832]; "material sample derivation association" -> object [color=blue, label=object, - lp="2850.4,178", - pos="e,2820.8,108.09 1680.4,251.75 1704,249.88 1728.4,248.18 1751.4,247 1808.3,244.08 2723.9,248.74 2777.4,229 2819.9,213.32 2825.1,186.96 \ -2830.4,142 2831.2,135.38 2832.3,133.39 2830.4,127 2829.4,123.55 2827.9,120.13 2826.1,116.85", + lp="4583.4,178", + pos="e,4552.8,108.09 2596.6,251.67 2620.4,249.78 2645.2,248.1 2668.4,247 2719.3,244.59 4454.9,244.84 4503.4,229 4527.3,221.18 4535.3,\ +216.87 4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,\ +116.85", style=solid]; predicate [height=0.5, - pos="2961.4,178", + pos="4693.4,178", width=1.5165]; "material sample derivation association" -> predicate [color=blue, label=predicate, - lp="2934.4,221.5", - pos="e,2937.6,194.3 1680.4,251.73 1704,249.85 1728.4,248.16 1751.4,247 1874.3,240.79 2738.7,257.54 2858.4,229 2883.3,223.07 2909.1,210.48 \ -2928.7,199.41", + lp="4666.4,221.5", + pos="e,4669.6,194.35 2596.6,251.66 2620.4,249.77 2645.2,248.09 2668.4,247 2775.1,241.97 4486.4,253.41 4590.4,229 4615.3,223.15 4641.2,\ +210.56 4660.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1798.4,265", + pos="2715.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1929.4,265", + pos="2846.4,265", width=2.0762]; subject -> object [label=relation, - lp="2802.4,134.5", - pos="e,2789.5,107.23 2765.5,159.55 2766.7,149.57 2769.2,137.07 2774.4,127 2776.6,122.68 2779.5,118.52 2782.7,114.66"]; + lp="4534.4,134.5", + pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; relation [height=0.5, - pos="2752.4,18", + pos="4484.4,18", width=1.2999]; - subject -> relation [pos="e,2753.7,36.188 2763.1,159.79 2761,132.48 2757,78.994 2754.5,46.38", + subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", style=dotted]; "material sample derivation association_subject" [color=blue, height=0.5, label="material sample", - pos="2108.4,265", + pos="3025.4,265", width=2.3831]; - object -> relation [pos="e,2765.2,35.54 2794.9,73.889 2788,64.939 2779.2,53.617 2771.4,43.584", + object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", style=dotted]; "material sample derivation association_object" [color=blue, height=0.5, label="named thing", - pos="2281.4,265", + pos="3198.4,265", width=1.9318]; "material sample derivation association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2447.4,265", + pos="3364.4,265", width=2.1665]; } diff --git a/graphviz/material_sample_derivation_association.svg b/graphviz/material_sample_derivation_association.svg index 33b9a5d905..2066aeaab8 100644 --- a/graphviz/material_sample_derivation_association.svg +++ b/graphviz/material_sample_derivation_association.svg @@ -4,16 +4,16 @@ - + %3 - + material sample derivation association - -material sample derivation association + +material sample derivation association @@ -24,9 +24,9 @@ material sample derivation association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ material sample derivation association->id - - -id + + +id @@ -50,9 +50,9 @@ material sample derivation association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ material sample derivation association->name - - -name + + +name @@ -76,9 +76,9 @@ material sample derivation association->description - - -description + + +description @@ -89,9 +89,9 @@ material sample derivation association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ material sample derivation association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ material sample derivation association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ material sample derivation association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ material sample derivation association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ material sample derivation association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ material sample derivation association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ material sample derivation association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ material sample derivation association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ material sample derivation association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ material sample derivation association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ material sample derivation association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +material sample derivation association->subject category + + +subject category + + + +object category + +ontology class + + + +material sample derivation association->object category + + +object category + + + +subject closure + +string + + + +material sample derivation association->subject closure + + +subject closure + + + +object closure + +string + + + +material sample derivation association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +material sample derivation association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +material sample derivation association->object category closure + + +object category closure + + + +subject namespace + +string + + + +material sample derivation association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +material sample derivation association->object namespace + + +object namespace + + + +subject label closure + +string + + + +material sample derivation association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +material sample derivation association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +material sample derivation association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + material sample derivation association->type - - -type + + +type - + category - -category + +category - + material sample derivation association->category - - -category + + +category - + subject - -subject + +subject - + material sample derivation association->subject - - -subject + + +subject - + object - -object + +object - + material sample derivation association->object - - -object + + +object - + predicate - -predicate + +predicate - + material sample derivation association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + material sample derivation association_subject - -material sample + +material sample - + object->relation - - + + - + material sample derivation association_object - -named thing + +named thing - + material sample derivation association_predicate - -predicate type + +predicate type diff --git a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv index b8bf9f517c..fd91f4da44 100644 --- a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv @@ -1,30 +1,29 @@ digraph { - graph [bb="0,0,4196.7,283"]; + graph [bb="0,0,5883.7,283"]; node [label="\N"]; "material sample to disease or phenotypic feature association" [height=0.5, label="material sample to disease or phenotypic feature association", - pos="2303.4,265", + pos="3267.4,265", width=8.1604]; association [height=0.5, pos="62.394,178", width=1.7332]; "material sample to disease or phenotypic feature association" -> association [label=is_a, - lp="813.39,221.5", - pos="e,106.46,190.89 2022.7,259.67 1720.5,254.49 1225.8,244.52 799.39,229 503.23,218.22 426.76,238.02 133.39,196 127.91,195.21 122.22,\ + lp="806.39,221.5", + pos="e,106.46,190.89 2974.9,263.26 2511.7,261.32 1581.1,254.32 792.39,229 499.29,219.59 423.68,237.65 133.39,196 127.91,195.21 122.22,\ 194.2 116.56,193.06"]; "material sample to entity association mixin" [height=0.5, pos="354.39,178", width=5.8856]; "material sample to disease or phenotypic feature association" -> "material sample to entity association mixin" [label=uses, - lp="1103.9,221.5", - pos="e,504.16,190.77 2027.1,258.85 1780.6,253.58 1409.8,244.02 1087.4,229 859.61,218.38 802.85,212.08 575.39,196 555.6,194.6 534.82,193.08 \ -514.24,191.53"]; + lp="1101.9,221.5", + pos="e,498.51,191.25 2973.9,263.81 2554.8,262.52 1760.9,256.26 1085.4,229 885.98,220.95 656.42,203.99 508.57,192.06"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="858.39,178", width=7.6188]; "material sample to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, - lp="1287.9,221.5", - pos="e,965.97,194.61 2017.2,260.94 1809.9,257.1 1523,248.46 1271.4,229 1171.5,221.27 1058.6,207.24 976.13,196"]; + lp="1285.9,221.5", + pos="e,962.42,194.68 2976,262.61 2503.8,259.73 1591.9,251.38 1269.4,229 1168.7,222.01 1054.9,207.65 972.55,196.11"]; id [color=blue, height=0.5, label=string, @@ -32,9 +31,9 @@ digraph { width=1.0652]; "material sample to disease or phenotypic feature association" -> id [color=blue, label=id, - lp="1409.4,221.5", - pos="e,1218.4,190.01 2031.4,258.17 1811.4,252.58 1519.6,242.91 1402.4,229 1328.1,220.19 1309.5,215.87 1237.4,196 1234.3,195.14 1231.1,\ -194.18 1227.9,193.17", + lp="1404.4,221.5", + pos="e,1218.4,189.98 2979.1,261.53 2493.3,256.94 1549.6,245.98 1397.4,229 1325.2,220.95 1307.3,215.5 1237.4,196 1234.3,195.13 1231.1,\ +194.17 1227.9,193.15", style=solid]; iri [color=blue, height=0.5, @@ -43,9 +42,9 @@ digraph { width=1.2277]; "material sample to disease or phenotypic feature association" -> iri [color=blue, label=iri, - lp="1522.4,221.5", - pos="e,1323.3,190.23 2015.4,261.33 1865.6,257.38 1679.7,248.51 1514.4,229 1437.5,219.93 1418.4,215.19 1343.4,196 1340,195.14 1336.5,194.18 \ -1333.1,193.17", + lp="1511.4,221.5", + pos="e,1323.3,190.16 2973.3,264.7 2547.2,264.59 1779,259.89 1503.4,229 1431.2,220.91 1413.6,214.45 1343.4,196 1340,195.11 1336.5,194.14 \ +1333.1,193.12", style=solid]; name [color=blue, height=0.5, @@ -54,8 +53,8 @@ digraph { width=1.5707]; "material sample to disease or phenotypic feature association" -> name [color=blue, label=name, - lp="1624.4,221.5", - pos="e,1447.8,191.29 2044.5,256.43 1881.4,250.62 1686.8,241.47 1604.4,229 1553.5,221.3 1496.7,205.93 1457.6,194.25", + lp="1615.4,221.5", + pos="e,1446.3,191.75 2978.2,261.75 2535.7,257.72 1727.8,247.9 1595.4,229 1546.9,222.08 1493.1,206.72 1455.8,194.84", style=solid]; description [color=blue, height=0.5, @@ -64,8 +63,8 @@ digraph { width=2.0943]; "material sample to disease or phenotypic feature association" -> description [color=blue, label=description, - lp="1738.9,221.5", - pos="e,1592.9,194.13 2045.2,256.4 1911.8,251.01 1763.5,242.31 1698.4,229 1665.3,222.23 1629.4,209.18 1602.4,198.11", + lp="1731.9,221.5", + pos="e,1590.8,194.37 2975.6,262.86 2554.5,260.4 1813.3,252.71 1691.4,229 1659.7,222.84 1625.7,209.79 1600.1,198.56", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,8 +73,8 @@ digraph { width=1.4443]; "material sample to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1875.4,221.5", - pos="e,1732.6,193.33 2073.9,253.75 1976.6,248.03 1875,239.84 1828.4,229 1798.3,221.99 1765.9,208.73 1741.8,197.62", + lp="1870.4,221.5", + pos="e,1730.9,193.52 2975.7,262.73 2586.2,260.14 1932.4,252.34 1823.4,229 1794.1,222.73 1763,209.39 1739.9,198.06", style=solid]; subject [color=blue, height=0.5, @@ -84,8 +83,8 @@ digraph { width=1.9318]; "material sample to disease or phenotypic feature association" -> subject [color=blue, label=subject, - lp="1998.4,221.5", - pos="e,1876,194.08 2104.6,251.68 2060.7,246.55 2014.6,239.29 1972.4,229 1942.4,221.7 1910.1,209.01 1885.4,198.25", + lp="1997.4,221.5", + pos="e,1874.5,194.33 2979,261.5 2627.1,257.62 2067,248.47 1971.4,229 1941,222.8 1908.4,209.83 1883.9,198.66", style=solid]; predicate [color=blue, height=0.5, @@ -95,7 +94,7 @@ digraph { "material sample to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, lp="2076.4,221.5", - pos="e,2016.9,196.2 2122.8,250.76 2087.9,245.66 2057.5,238.64 2042.4,229 2033.5,223.33 2026.6,214.19 2021.5,205.27", + pos="e,2016.4,196.12 2976.5,262.49 2627,259.67 2082.4,251.65 2042.4,229 2033,223.67 2025.9,214.3 2020.8,205.1", style=solid]; object [color=blue, height=0.5, @@ -105,7 +104,7 @@ digraph { "material sample to disease or phenotypic feature association" -> object [color=blue, label=object, lp="2155.4,178", - pos="e,1984,105.47 2245.5,247.33 2211.2,235.93 2167.9,218.75 2133.4,196 2114.5,183.54 2116.1,172.77 2097.4,160 2065.3,138.07 2025,120.64 \ + pos="e,1984,105.47 2991,258.86 2679.9,251.27 2207.9,233.7 2133.4,196 2113.2,185.78 2116.1,172.77 2097.4,160 2065.3,138.07 2025,120.64 \ 1993.5,108.92", style=solid]; negated [color=blue, @@ -115,8 +114,8 @@ digraph { width=1.2999]; "material sample to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2302.4,221.5", - pos="e,2246.8,195.31 2289.2,246.8 2278.9,234.23 2264.7,217.01 2253.2,203.08", + lp="2457.4,221.5", + pos="e,2267.8,190.38 2995.2,258.22 2792.8,252.87 2534,243.52 2428.4,229 2375.7,221.75 2316.7,205.44 2277.5,193.41", style=solid]; qualifiers [color=blue, height=0.5, @@ -125,8 +124,8 @@ digraph { width=2.1304]; "material sample to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2381.9,221.5", - pos="e,2361.7,195.93 2319.6,246.79 2324.8,241.2 2330.4,234.91 2335.4,229 2342.1,221.01 2349.3,212.07 2355.5,203.97", + lp="2588.9,221.5", + pos="e,2415.9,193.28 3003.6,257.08 2837.5,251.54 2639.2,242.46 2555.4,229 2510.8,221.84 2461.5,207.79 2425.6,196.41", style=solid]; publications [color=blue, height=0.5, @@ -135,8 +134,8 @@ digraph { width=1.7332]; "material sample to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2498.4,221.5", - pos="e,2500.9,193.86 2363.8,247.36 2381.8,241.96 2401.6,235.64 2419.4,229 2443.8,219.91 2470.4,208.1 2491.6,198.24", + lp="2723.4,221.5", + pos="e,2565.1,193.26 3016.2,255.66 2886.6,250.04 2742.8,241.36 2679.4,229 2643.2,221.93 2603.6,208.25 2574.5,196.98", style=solid]; "has evidence" [color=blue, height=0.5, @@ -145,8 +144,8 @@ digraph { width=2.0943]; "material sample to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2640.9,221.5", - pos="e,2651.5,193.96 2440.5,249.08 2475.3,243.97 2512.5,237.37 2546.4,229 2579,220.96 2614.5,208.31 2641.8,197.75", + lp="2864.9,221.5", + pos="e,2719.7,194.32 3008.2,256.5 2945.5,251.21 2879.1,242.66 2818.4,229 2787.5,222.06 2754.3,209.29 2729,198.39", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -155,8 +154,8 @@ digraph { width=3.015]; "material sample to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2827.9,221.5", - pos="e,2839,194.07 2504.8,251.89 2565.1,246.64 2631.1,239.26 2691.4,229 2738.1,221.05 2789.9,207.79 2828.9,196.92", + lp="2997.9,221.5", + pos="e,2899.8,196.41 3047.1,253.05 2998.6,247.87 2955.2,240.24 2933.4,229 2922.5,223.39 2913.2,213.9 2905.9,204.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -165,8 +164,8 @@ digraph { width=3.015]; "material sample to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3074.4,221.5", - pos="e,3069.5,193.57 2510.2,252.17 2677.4,242.55 2886.6,230.35 2896.4,229 2952.1,221.29 3014.4,207.24 3059.8,196", + lp="3164.4,221.5", + pos="e,3087.8,195.17 3115.3,249.59 3094.1,244.63 3076.9,237.96 3069.4,229 3061,218.96 3067.9,209.01 3079.3,200.67", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -175,9 +174,8 @@ digraph { width=3.015]; "material sample to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3347.9,221.5", - pos="e,3313.8,194.43 2505.9,251.96 2539.4,250.16 2573.9,248.43 2606.4,247 2732.3,241.47 3048.7,247.49 3173.4,229 3218,222.39 3267.2,208.87 \ -3303.8,197.56", + lp="3374.9,221.5", + pos="e,3294.9,192.66 3263.2,246.77 3261.8,236.38 3261.8,223.38 3268.4,214 3273,207.37 3279.1,202 3286,197.65", style=solid]; timepoint [color=blue, height=0.5, @@ -186,9 +184,8 @@ digraph { width=1.5346]; "material sample to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3527.4,221.5", - pos="e,3521.7,194.98 2503.4,251.79 2537.8,249.97 2573.1,248.29 2606.4,247 2701,243.35 3367.4,255.32 3458.4,229 3478.1,223.29 3497.9,211.66 \ -3513.2,201.06", + lp="3536.4,221.5", + pos="e,3524.1,195.19 3419.2,249.53 3440.6,244.54 3462,237.88 3481.4,229 3489.1,225.48 3503.6,213.47 3516.4,202.1", style=solid]; "original subject" [color=blue, height=0.5, @@ -197,49 +194,168 @@ digraph { width=1.0652]; "material sample to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3658.4,221.5", - pos="e,3634.3,193.79 2502.6,251.76 2537.2,249.94 2572.8,248.26 2606.4,247 2659.7,245.01 3515,243.24 3566.4,229 3587.8,223.08 3609.4,210.66 \ -3625.8,199.69", + lp="3653.4,221.5", + pos="e,3631.3,192.7 3445.6,250.64 3498.9,245.12 3549.7,237.91 3574.4,229 3585.9,224.86 3587.1,220.57 3597.4,214 3605.6,208.79 3614.4,\ +203.21 3622.7,198.07", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3768.4,178", + pos="3767.4,178", width=1.5887]; "material sample to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3804.9,221.5", - pos="e,3757,195.87 2502.2,251.71 2536.9,249.89 2572.7,248.22 2606.4,247 2668.1,244.77 3661.5,253.11 3718.4,229 3730.9,223.69 3742,213.59 \ -3750.5,203.85", + lp="3793.9,221.5", + pos="e,3750.8,195.38 3484,252.84 3584.9,246.53 3687.6,238.1 3709.4,229 3717.1,225.8 3731.1,213.8 3743.4,202.35", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3918.4,178", + pos="3881.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3944.9,221.5", - pos="e,3908.2,195.85 2501.4,251.7 2536.3,249.86 2572.4,248.19 2606.4,247 2641.5,245.76 3840.3,243.36 3872.4,229 3884.2,223.71 3894.4,\ -213.76 3902.1,204.11", + lp="3923.9,221.5", + pos="e,3878.5,196.31 3476,252.29 3645.6,242.67 3857.4,230.41 3859.4,229 3867.2,223.57 3872.3,214.72 3875.5,205.97", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="4014.4,178", + width=2.1304]; + "material sample to disease or phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="4055.9,221.5", + pos="e,4007.4,196.1 3473.2,252.12 3505.7,250.34 3539,248.57 3570.4,247 3615.8,244.73 3939.5,250.89 3979.4,229 3989.1,223.65 3996.8,214.27 \ +4002.4,205.08", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="4185.4,178", + width=2.1304]; + "material sample to disease or phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="4202.9,221.5", + pos="e,4169.5,195.61 3470.3,251.96 3503.7,250.17 3538,248.44 3570.4,247 3631.4,244.29 4061.9,249.39 4119.4,229 4135.1,223.42 4150.2,212.61 \ +4161.9,202.46", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="4318.4,178", + width=1.0652]; + "material sample to disease or phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="4336.9,221.5", + pos="e,4303,194.73 3468.6,251.86 3502.6,250.06 3537.5,248.35 3570.4,247 3608.8,245.42 4225.6,243 4261.4,229 4269.2,225.94 4283.4,213.52 \ +4295.6,201.83", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4414.4,178", + width=1.0652]; + "material sample to disease or phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4456.4,221.5", + pos="e,4412,196.42 3467.4,251.81 3501.8,249.99 3537.1,248.3 3570.4,247 3593.2,246.11 4374.5,241.86 4393.4,229 4401.2,223.69 4406.1,214.87 \ +4409.2,206.1", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4547.4,178", + width=2.1304]; + "material sample to disease or phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4614.9,221.5", + pos="e,4539.8,196.22 3467,251.75 3501.5,249.94 3537,248.26 3570.4,247 3622.6,245.04 4464,252.95 4510.4,229 4520.6,223.75 4528.7,214.26 \ +4534.7,204.95", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4736.4,178", + width=2.1304]; + "material sample to disease or phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4804.9,221.5", + pos="e,4731.1,196.13 3465.8,251.72 3500.6,249.89 3536.6,248.22 3570.4,247 3601.9,245.87 4679.1,244.77 4706.4,229 4715.5,223.75 4722.2,\ +214.52 4726.9,205.41", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4926.4,178", + width=1.0652]; + "material sample to disease or phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4976.4,221.5", + pos="e,4919.7,196.21 3465.4,251.68 3500.3,249.85 3536.4,248.18 3570.4,247 3607.1,245.72 4860.1,246.4 4892.4,229 4902.1,223.78 4909.6,\ +214.43 4915,205.21", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="5085.4,178", + width=1.0652]; + "material sample to disease or phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="5129.4,221.5", + pos="e,5078,195.76 3465,251.66 3500.1,249.83 3536.3,248.16 3570.4,247 3611.4,245.6 5011.8,247.7 5048.4,229 5058.7,223.71 5066.9,214.03 \ +5072.9,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="5236.4,178", + width=1.0652]; + "material sample to disease or phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="5289.4,221.5", + pos="e,5228.4,195.79 3464.6,251.65 3499.8,249.81 3536.2,248.15 3570.4,247 3615.6,245.48 5156.9,249.05 5197.4,229 5208.1,223.69 5216.8,\ +213.87 5223.2,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5407.4,178", + width=1.0652]; + "material sample to disease or phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5455.9,221.5", + pos="e,5399.1,195.8 3464.6,251.62 3499.8,249.78 3536.2,248.13 3570.4,247 3620.3,245.35 5322.5,250.85 5367.4,229 5378.3,223.71 5387.1,\ +213.9 5393.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5569.4,178", + width=2.347]; + "material sample to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5617.9,221.5", + pos="e,5560.8,196.3 3464.1,251.62 3499.5,249.78 3536,248.12 3570.4,247 3624.8,245.23 5480.5,252.8 5529.4,229 5540.1,223.79 5548.9,214.18 \ +5555.4,204.76", style=solid]; type [height=0.5, - pos="4044.4,178", + pos="5731.4,178", width=0.86659]; "material sample to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="4037.4,221.5", - pos="e,4035.2,195.34 2501.4,251.66 2536.3,249.83 2572.4,248.17 2606.4,247 2645.1,245.67 3965.2,245.18 4000.4,229 4012.1,223.62 4021.9,\ -213.46 4029.3,203.69", + lp="5726.4,221.5", + pos="e,5723.1,195.81 3464.1,251.6 3499.5,249.76 3536,248.11 3570.4,247 3599.8,246.05 5664.9,241.87 5691.4,229 5702.3,223.72 5711.1,213.91 \ +5717.7,204.36", style=solid]; category [height=0.5, - pos="4145.4,178", + pos="5832.4,178", width=1.4263]; "material sample to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="4123.9,221.5", - pos="e,4125,194.56 2501,251.67 2536.1,249.83 2572.3,248.17 2606.4,247 2687,244.24 3979.6,250.08 4057.4,229 4078.6,223.26 4100,211.23 \ -4116.5,200.4", + lp="5812.9,221.5", + pos="e,5812.2,194.83 3464.1,251.59 3499.5,249.75 3536,248.11 3570.4,247 3630.8,245.06 5688.1,244.97 5746.4,229 5767.1,223.34 5787.9,211.43 \ +5803.9,200.65", style=solid]; subject -> object [label=relation, lp="1927.4,134.5", @@ -254,11 +370,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2653.4,265", + pos="3617.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2784.4,265", + pos="3748.4,265", width=2.0762]; } diff --git a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg index 6421ff7d2d..aa4cfbf6cf 100644 --- a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + material sample to disease or phenotypic feature association - -material sample to disease or phenotypic feature association + +material sample to disease or phenotypic feature association @@ -24,9 +24,9 @@ material sample to disease or phenotypic feature association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ material sample to disease or phenotypic feature association->material sample to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ material sample to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ material sample to disease or phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ material sample to disease or phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ material sample to disease or phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ material sample to disease or phenotypic feature association->description - - -description + + +description @@ -115,9 +115,9 @@ material sample to disease or phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ material sample to disease or phenotypic feature association->subject - - -subject + + +subject @@ -141,8 +141,8 @@ material sample to disease or phenotypic feature association->predicate - - + + predicate @@ -154,7 +154,7 @@ material sample to disease or phenotypic feature association->object - + object @@ -167,9 +167,9 @@ material sample to disease or phenotypic feature association->negated - - -negated + + +negated @@ -180,9 +180,9 @@ material sample to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -193,9 +193,9 @@ material sample to disease or phenotypic feature association->publications - - -publications + + +publications @@ -206,9 +206,9 @@ material sample to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -219,9 +219,9 @@ material sample to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -232,9 +232,9 @@ material sample to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -245,9 +245,9 @@ material sample to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -258,9 +258,9 @@ material sample to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -271,98 +271,241 @@ material sample to disease or phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie material sample to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string material sample to disease or phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +material sample to disease or phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +material sample to disease or phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +material sample to disease or phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +material sample to disease or phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +material sample to disease or phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +material sample to disease or phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +material sample to disease or phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +material sample to disease or phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +material sample to disease or phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +material sample to disease or phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +material sample to disease or phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + material sample to disease or phenotypic feature association->type - - -type + + +type - + category - -category + +category - + material sample to disease or phenotypic feature association->category - - -category + + +category - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/molecular_activity_to_chemical_entity_association.gv b/graphviz/molecular_activity_to_chemical_entity_association.gv index badb50f2a8..0b883f073c 100644 --- a/graphviz/molecular_activity_to_chemical_entity_association.gv +++ b/graphviz/molecular_activity_to_chemical_entity_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "molecular activity to chemical entity association" [height=0.5, label="molecular activity to chemical entity association", - pos="1542.4,265", + pos="2492.4,265", width=6.5355]; association [height=0.5, pos="62.394,178", width=1.7332]; "molecular activity to chemical entity association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1308,263.42 996.52,261.64 463.15,254.77 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2258.1,263.28 1726.5,261.21 460.31,253.73 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "molecular activity to chemical entity association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1311.5,261.44 1029,257.52 567.17,248.35 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,194.16 \ -219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2258.9,262.54 1750.1,259 572.49,248.78 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular activity to chemical entity association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1316,260.04 1062.6,254.93 667.94,244.78 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,194.19 \ -324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2259.9,262.15 1773.1,257.95 677.2,246.65 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ +194.18 325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "molecular activity to chemical entity association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1315.8,260.11 1086,255.33 746.39,245.71 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2259.2,262.45 1790.8,258.93 766.83,249.04 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "molecular activity to chemical entity association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1314.2,260.47 1111.6,256.2 831.09,247.19 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2258.4,262.99 1810.5,260.52 863.43,252.56 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "molecular activity to chemical entity association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1324.8,258.13 1161.9,252.71 953.1,243.31 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2259.4,262.39 1842.5,259.01 999.89,249.69 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "molecular activity to chemical entity association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1325.1,258.04 1234.7,253.23 1129,244.57 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2257,264.77 1907.5,264.81 1268,260.37 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "molecular activity to chemical entity association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1367.1,252.99 1305.3,247.64 1235.5,239.93 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2258.2,263.06 1940.8,260.87 1390.8,253.53 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "molecular activity to chemical entity association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1409.9,250.12 1370.3,244.81 1326.9,237.85 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2258.3,263.1 1970,260.93 1497.3,253.59 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "molecular activity to chemical entity association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1462.1,248.05 1439.9,242.83 1416,236.43 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2258.5,262.94 2001.1,260.57 1604.1,252.98 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "molecular activity to chemical entity association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461.1,195.6 1522,246.8 1506.7,233.96 1485.7,216.27 1468.9,202.19", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2261.5,261.53 2041.8,257.97 1727.5,249.4 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "molecular activity to chemical entity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.7,246.95 1579,241.56 1587.8,235.35 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2257.2,264.2 2073,262.28 1832.7,254.63 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "molecular activity to chemical entity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1650.9,249 1681.4,243.76 1714.4,237.11 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2272.6,258.53 2101.7,253.17 1891.2,243.64 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,8 +140,8 @@ digraph { width=3.015]; "molecular activity to chemical entity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.5,195.15 1706.4,252.09 1826,243.22 1969.6,232.13 1983.4,229 2013.2,222.24 2045.2,209.99 2070,199.31", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2273.7,258.34 2180.2,253.61 2089,244.93 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -150,9 +150,8 @@ digraph { width=1.5346]; "molecular activity to chemical entity association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.74 1705.4,252 1732.8,250.18 1760.9,248.44 1787.4,247 1838.6,244.23 2201.8,250.26 2248.4,229 2260.4,223.52 2270.9,213.4 \ -2278.8,203.69", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2349.5,250.63 2325.6,245.57 2305.8,238.6 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -161,9 +160,8 @@ digraph { width=1.0652]; "molecular activity to chemical entity association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.21 1704.4,251.91 1732.1,250.09 1760.6,248.37 1787.4,247 1849,243.86 2284.3,249.81 2342.4,229 2351.2,225.84 2368.1,212.71 \ -2382.5,200.7", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2397.4,248.51 2388.5,243.59 2380.5,237.22 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -172,85 +170,202 @@ digraph { width=1.5887]; "molecular activity to chemical entity association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.23 1703.1,251.85 1731.2,250.01 1760.1,248.3 1787.4,247 1825.9,245.16 2446.9,246.16 2481.4,229 2492.1,223.7 2500.8,214.07 \ -2507.4,204.67", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.98 1702.5,251.78 1730.7,249.94 1759.9,248.25 1787.4,247 1810.8,245.94 2610.8,241.85 2630.4,229 2638.5,223.67 2643.8,\ -214.68 2647.3,205.78", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2590.7,248.54 2601.6,243.65 2611.9,237.29 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "molecular activity to chemical entity association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2651.6,251.7 2688.6,246.5 2721.8,239.2 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "molecular activity to chemical entity association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.4,195.77 2664.7,252.72 2756.8,245.89 2855.2,236.99 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "molecular activity to chemical entity association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.17 2659.4,252.3 2685.5,250.5 2712.2,248.69 2737.4,247 2799.4,242.85 2959.1,253 3016.4,229 3030.2,223.22 3042.9,212.58 \ +3052.7,202.59", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "molecular activity to chemical entity association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.32 2656.1,252.05 2683.2,250.24 2711.1,248.48 2737.4,247 2760.4,245.7 3133.6,242.35 3152.4,229 3160,223.64 3164.7,214.92 \ +3167.6,206.26", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "molecular activity to chemical entity association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.16 2654.4,251.94 2682.1,250.12 2710.6,248.38 2737.4,247 2766.9,245.48 3242.3,242.73 3268.4,229 3278.5,223.67 3286.6,\ +214.17 3292.6,204.87", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "molecular activity to chemical entity association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.15 2653.1,251.82 2681.2,249.99 2710.1,248.28 2737.4,247 2777.8,245.1 3429.1,248.58 3464.4,229 3473.9,223.71 3481.2,\ +214.34 3486.5,205.14", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "molecular activity to chemical entity association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2652.1,251.77 2680.5,249.92 2709.8,248.23 2737.4,247 2788.1,244.74 3606.4,252.6 3651.4,229 3661.6,223.65 3669.6,\ +213.97 3675.4,204.53", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "molecular activity to chemical entity association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.75 2651.8,251.72 2680.3,249.88 2709.7,248.19 2737.4,247 2767.1,245.72 3781.9,242.45 3808.4,229 3818.9,223.7 3827.2,\ +214.02 3833.4,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "molecular activity to chemical entity association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.77 2651.5,251.7 2680.1,249.85 2709.6,248.17 2737.4,247 2771.3,245.58 3928,244.11 3958.4,229 3969.1,223.67 3977.8,213.85 \ +3984.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "molecular activity to chemical entity association" -> "object label closure" [color=blue, + label="object label closure", + lp="4215.9,221.5", + pos="e,4160.1,195.79 2651.1,251.68 2679.8,249.82 2709.5,248.15 2737.4,247 2776,245.41 4093.7,245.96 4128.4,229 4139.3,223.69 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "molecular activity to chemical entity association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.5,196.3 2650.8,251.67 2679.6,249.81 2709.4,248.13 2737.4,247 2780.5,245.26 4250.5,247.67 4289.4,229 4300.2,223.79 4309.2,\ +214.18 4315.9,204.76", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "molecular activity to chemical entity association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1702.1,251.74 1730.5,249.9 1759.8,248.21 1787.4,247 1814.1,245.82 2731.7,248.09 2750.4,229 2756.6,222.69 2756.6,\ -213.65 2754.2,204.99", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2650.5,251.66 2679.4,249.8 2709.3,248.12 2737.4,247 2761.2,246.05 4433.8,243.85 4452.4,229 4459.2,223.54 4462.6,\ +214.92 4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "molecular activity to chemical entity association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.86 1701.8,251.75 1730.3,249.9 1759.7,248.21 1787.4,247 1843.2,244.57 2741,250.83 2792.4,229 2804.9,223.68 2816,213.58 \ -2824.5,203.84", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2650.5,251.66 2679.4,249.79 2709.3,248.12 2737.4,247 2786.3,245.06 4452,244.65 4498.4,229 4514.6,223.53 4530.1,212.5 \ +4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "molecular activity to chemical entity association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.75 1701.5,251.74 1730.1,249.88 1759.6,248.19 1787.4,247 1848.2,244.39 2824.4,247.29 2882.4,229 2900.4,223.33 2918,211.74 \ -2931.5,201.15", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2650.5,251.64 2679.4,249.78 2709.3,248.11 2737.4,247 2840.5,242.93 4495,256.59 4594.4,229 4615.1,223.24 4636,211.08 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "molecular activity to chemical entity association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1701.5,251.71 1730.1,249.86 1759.6,248.18 1787.4,247 1853,244.23 2907.8,251.67 2969.4,229 3011.9,213.37 3017.1,186.96 \ -3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2650.5,251.63 2679.4,249.77 2709.3,248.1 2737.4,247 2791.5,244.88 4633.9,245.54 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1834.4,265", + pos="2784.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1965.4,265", + pos="2915.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "molecular activity to chemical entity association_subject" [color=blue, height=0.5, label="molecular activity", - pos="2152.4,265", + pos="3102.4,265", width=2.6178]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "molecular activity to chemical entity association_object" [color=blue, height=0.5, label="chemical entity", - pos="2346.4,265", + pos="3296.4,265", width=2.2748]; } diff --git a/graphviz/molecular_activity_to_chemical_entity_association.svg b/graphviz/molecular_activity_to_chemical_entity_association.svg index 711df9dff2..36e1ee2bcb 100644 --- a/graphviz/molecular_activity_to_chemical_entity_association.svg +++ b/graphviz/molecular_activity_to_chemical_entity_association.svg @@ -4,16 +4,16 @@ - + %3 - + molecular activity to chemical entity association - -molecular activity to chemical entity association + +molecular activity to chemical entity association @@ -24,9 +24,9 @@ molecular activity to chemical entity association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ molecular activity to chemical entity association->id - - -id + + +id @@ -50,9 +50,9 @@ molecular activity to chemical entity association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular activity to chemical entity association->name - - -name + + +name @@ -76,9 +76,9 @@ molecular activity to chemical entity association->description - - -description + + +description @@ -89,9 +89,9 @@ molecular activity to chemical entity association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ molecular activity to chemical entity association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ molecular activity to chemical entity association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ molecular activity to chemical entity association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ molecular activity to chemical entity association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ molecular activity to chemical entity association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ molecular activity to chemical entity association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ molecular activity to chemical entity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ molecular activity to chemical entity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ molecular activity to chemical entity association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ molecular activity to chemical entity association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ molecular activity to chemical entity association->original predicate - - -original predicate + + +original predicate original object - -string + +string molecular activity to chemical entity association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +molecular activity to chemical entity association->subject category + + +subject category + + + +object category + +ontology class + + + +molecular activity to chemical entity association->object category + + +object category + + + +subject closure + +string + + + +molecular activity to chemical entity association->subject closure + + +subject closure + + + +object closure + +string + + + +molecular activity to chemical entity association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +molecular activity to chemical entity association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +molecular activity to chemical entity association->object category closure + + +object category closure + + + +subject namespace + +string + + + +molecular activity to chemical entity association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +molecular activity to chemical entity association->object namespace + + +object namespace + + + +subject label closure + +string + + + +molecular activity to chemical entity association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +molecular activity to chemical entity association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +molecular activity to chemical entity association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + molecular activity to chemical entity association->type - - -type + + +type - + category - -category + +category - + molecular activity to chemical entity association->category - - -category + + +category - + subject - -subject + +subject - + molecular activity to chemical entity association->subject - - -subject + + +subject - + object - -object + +object - + molecular activity to chemical entity association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + molecular activity to chemical entity association_subject - -molecular activity + +molecular activity - + object->relation - - + + - + molecular activity to chemical entity association_object - -chemical entity + +chemical entity diff --git a/graphviz/molecular_activity_to_molecular_activity_association.gv b/graphviz/molecular_activity_to_molecular_activity_association.gv index 19e17fb7b8..69f54a6cde 100644 --- a/graphviz/molecular_activity_to_molecular_activity_association.gv +++ b/graphviz/molecular_activity_to_molecular_activity_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "molecular activity to molecular activity association" [height=0.5, label="molecular activity to molecular activity association", - pos="1542.4,265", + pos="2492.4,265", width=6.8605]; association [height=0.5, pos="62.394,178", width=1.7332]; "molecular activity to molecular activity association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1296.3,263.35 983.37,261.47 460.75,254.45 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2246.6,263.23 1708.5,261.1 458.93,253.55 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "molecular activity to molecular activity association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1300.7,261.29 1017.4,257.29 565.01,248.1 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,\ -194.16 219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2247.8,262.46 1733.2,258.85 571.19,248.64 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular activity to molecular activity association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1305.8,259.83 1052.1,254.66 665.96,244.57 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,\ -194.19 324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2248.3,262.05 1755.9,257.77 675.86,246.51 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ +194.18 325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "molecular activity to molecular activity association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1305.4,259.9 1075.9,255.04 744.45,245.46 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2247.9,262.36 1774.6,258.77 765.56,248.88 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "molecular activity to molecular activity association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1303.9,260.25 1102.2,255.9 829.24,246.88 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2247,262.92 1794.7,260.38 862.19,252.36 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "molecular activity to molecular activity association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1315.6,257.82 1154.1,252.36 951.51,243.04 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2247.8,262.3 1827.1,258.84 998.67,249.5 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "molecular activity to molecular activity association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1316.9,257.6 1228.4,252.71 1126.2,244.1 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2245.4,264.77 1893.5,264.71 1265.5,260.02 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "molecular activity to molecular activity association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1362.9,252.62 1302.1,247.29 1234.1,239.68 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2246.8,262.98 1927.7,260.69 1388.4,253.24 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "molecular activity to molecular activity association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1408,249.86 1368.8,244.58 1326.2,237.7 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2246.6,263.01 1957.4,260.73 1495,253.26 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "molecular activity to molecular activity association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1461.7,247.96 1439.6,242.75 1415.9,236.38 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2247.2,262.84 1989.6,260.34 1601.9,252.63 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "molecular activity to molecular activity association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461.1,195.6 1522,246.8 1506.7,233.96 1485.7,216.27 1468.9,202.19", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2250.3,261.34 2031.3,257.67 1725.5,249.05 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "molecular activity to molecular activity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.7,246.95 1579,241.56 1587.8,235.35 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2245.5,264.07 2063,261.95 1830.7,254.09 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "molecular activity to molecular activity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1652,248.82 1682.2,243.61 1714.8,237.02 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2263.2,258.23 2094.1,252.82 1891,243.37 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,8 +140,8 @@ digraph { width=3.015]; "molecular activity to molecular activity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.5,195.15 1719.1,252.39 1830.3,244.67 1957.4,234.89 1983.4,229 2013.2,222.24 2045.2,209.99 2070,199.31", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2265.2,257.9 2174.7,253.08 2088.6,244.44 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -150,9 +150,8 @@ digraph { width=1.5346]; "molecular activity to molecular activity association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.74 1713.5,252.01 1741.8,250.21 1770.9,248.46 1798.4,247 1848.4,244.34 2202.9,249.78 2248.4,229 2260.4,223.51 2270.8,\ -213.39 2278.8,203.68", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2348.1,250.32 2324.8,245.29 2305.6,238.4 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -161,9 +160,8 @@ digraph { width=1.0652]; "molecular activity to molecular activity association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.21 1712.4,251.92 1741.1,250.1 1770.6,248.38 1798.4,247 1858.8,244 2285.5,249.42 2342.4,229 2351.2,225.84 2368.1,212.71 \ -2382.5,200.7", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2397.2,248.35 2388.3,243.45 2380.5,237.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -172,85 +170,201 @@ digraph { width=1.5887]; "molecular activity to molecular activity association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.23 1711,251.84 1740.2,250.02 1770.1,248.31 1798.4,247 1836.3,245.24 2447.4,245.89 2481.4,229 2492.1,223.7 2500.8,214.07 \ -2507.4,204.67", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.97 1710.3,251.77 1739.7,249.94 1769.9,248.25 1798.4,247 1821.5,245.98 2611.1,241.68 2630.4,229 2638.5,223.67 2643.8,\ -214.68 2647.3,205.78", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2591,248.4 2601.8,243.53 2612,237.21 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "molecular activity to molecular activity association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2654.2,251.34 2690.2,246.16 2722.2,238.96 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "molecular activity to molecular activity association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.4,195.77 2669,252.4 2759.8,245.62 2855.5,236.87 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "molecular activity to molecular activity association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.16 2667.9,252.32 2820.1,242.19 3016.1,229.11 3016.4,229 3030.2,223.21 3042.9,212.56 3052.7,202.58", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "molecular activity to molecular activity association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.32 2664.5,252.06 2692.5,250.26 2721.3,248.5 2748.4,247 2770.8,245.76 3134.1,242.01 3152.4,229 3160,223.63 3164.7,214.92 \ +3167.6,206.26", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "molecular activity to molecular activity association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.16 2662.8,251.93 2691.3,250.12 2720.7,248.4 2748.4,247 2777.3,245.54 3242.8,242.45 3268.4,229 3278.5,223.67 3286.6,\ +214.17 3292.6,204.87", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "molecular activity to molecular activity association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.15 2661,251.81 2690.2,249.99 2720.1,248.29 2748.4,247 2788.1,245.18 3429.6,248.3 3464.4,229 3473.9,223.7 3481.2,214.34 \ +3486.5,205.14", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "molecular activity to molecular activity association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2660,251.75 2689.4,249.92 2719.8,248.23 2748.4,247 2798.5,244.84 3607,252.32 3651.4,229 3661.6,223.65 3669.6,213.96 \ +3675.4,204.53", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "molecular activity to molecular activity association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.75 2659.3,251.72 2689,249.88 2719.6,248.2 2748.4,247 2777.8,245.77 3782.1,242.31 3808.4,229 3818.9,223.7 3827.2,214.02 \ +3833.4,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "molecular activity to molecular activity association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.77 2659,251.69 2688.7,249.85 2719.5,248.17 2748.4,247 2782,245.64 3928.3,243.97 3958.4,229 3969.1,223.67 3977.8,213.85 \ +3984.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "molecular activity to molecular activity association" -> "object label closure" [color=blue, + label="object label closure", + lp="4215.9,221.5", + pos="e,4160.1,195.79 2658.6,251.67 2688.5,249.82 2719.4,248.15 2748.4,247 2786.7,245.48 4094,245.83 4128.4,229 4139.3,223.69 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "molecular activity to molecular activity association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.5,196.3 2658.3,251.66 2688.2,249.81 2719.2,248.14 2748.4,247 2791.2,245.33 4250.8,247.54 4289.4,229 4300.2,223.79 4309.2,\ +214.18 4315.9,204.76", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "molecular activity to molecular activity association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1709.6,251.75 1739.2,249.91 1769.7,248.22 1798.4,247 1824.8,245.87 2731.9,247.88 2750.4,229 2756.6,222.69 2756.5,\ -213.65 2754.2,204.99", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2658.3,251.63 2688.2,249.78 2719.2,248.12 2748.4,247 2772,246.09 4433.9,243.75 4452.4,229 4459.2,223.54 4462.6,214.92 \ +4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "molecular activity to molecular activity association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.86 1709.6,251.73 1739.2,249.89 1769.7,248.21 1798.4,247 1853.6,244.67 2741.6,250.6 2792.4,229 2804.9,223.67 2816,213.58 \ -2824.5,203.84", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2658.3,251.62 2688.2,249.78 2719.2,248.12 2748.4,247 2797,245.14 4452.3,244.55 4498.4,229 4514.6,223.53 4530.1,212.5 \ +4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "molecular activity to molecular activity association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.75 1709.3,251.71 1739,249.87 1769.6,248.2 1798.4,247 1858.6,244.5 2825,247.11 2882.4,229 2900.4,223.32 2918,211.74 \ -2931.5,201.15", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2657.9,251.63 2688,249.78 2719.1,248.11 2748.4,247 2850.9,243.1 4495.6,256.43 4594.4,229 4615.1,223.24 4636,211.08 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "molecular activity to molecular activity association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1709,251.71 1738.7,249.86 1769.5,248.18 1798.4,247 1863.4,244.34 2908.3,251.47 2969.4,229 3011.9,213.36 3017.1,186.96 \ -3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2657.9,251.62 2688,249.77 2719.1,248.11 2748.4,247 2802.2,244.97 4634.2,245.45 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1845.4,265", + pos="2795.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1976.4,265", + pos="2926.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "molecular activity to molecular activity association_subject" [color=blue, height=0.5, label="molecular activity", - pos="2163.4,265", + pos="3113.4,265", width=2.6178]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "molecular activity to molecular activity association_object" [color=blue, height=0.5, label="molecular activity", - pos="2369.4,265", + pos="3319.4,265", width=2.6178]; } diff --git a/graphviz/molecular_activity_to_molecular_activity_association.svg b/graphviz/molecular_activity_to_molecular_activity_association.svg index 183e7db30f..1949412c8e 100644 --- a/graphviz/molecular_activity_to_molecular_activity_association.svg +++ b/graphviz/molecular_activity_to_molecular_activity_association.svg @@ -4,16 +4,16 @@ - + %3 - + molecular activity to molecular activity association - -molecular activity to molecular activity association + +molecular activity to molecular activity association @@ -24,9 +24,9 @@ molecular activity to molecular activity association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ molecular activity to molecular activity association->id - - -id + + +id @@ -50,9 +50,9 @@ molecular activity to molecular activity association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular activity to molecular activity association->name - - -name + + +name @@ -76,9 +76,9 @@ molecular activity to molecular activity association->description - - -description + + +description @@ -89,9 +89,9 @@ molecular activity to molecular activity association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ molecular activity to molecular activity association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ molecular activity to molecular activity association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ molecular activity to molecular activity association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ molecular activity to molecular activity association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ molecular activity to molecular activity association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ molecular activity to molecular activity association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ molecular activity to molecular activity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ molecular activity to molecular activity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ molecular activity to molecular activity association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ molecular activity to molecular activity association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ molecular activity to molecular activity association->original predicate - - -original predicate + + +original predicate original object - -string + +string molecular activity to molecular activity association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +molecular activity to molecular activity association->subject category + + +subject category + + + +object category + +ontology class + + + +molecular activity to molecular activity association->object category + + +object category + + + +subject closure + +string + + + +molecular activity to molecular activity association->subject closure + + +subject closure + + + +object closure + +string + + + +molecular activity to molecular activity association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +molecular activity to molecular activity association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +molecular activity to molecular activity association->object category closure + + +object category closure + + + +subject namespace + +string + + + +molecular activity to molecular activity association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +molecular activity to molecular activity association->object namespace + + +object namespace + + + +subject label closure + +string + + + +molecular activity to molecular activity association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +molecular activity to molecular activity association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +molecular activity to molecular activity association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + molecular activity to molecular activity association->type - - -type + + +type - + category - -category + +category - + molecular activity to molecular activity association->category - - -category + + +category - + subject - -subject + +subject - + molecular activity to molecular activity association->subject - - -subject + + +subject - + object - -object + +object - + molecular activity to molecular activity association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + molecular activity to molecular activity association_subject - -molecular activity + +molecular activity - + object->relation - - + + - + molecular activity to molecular activity association_object - -molecular activity + +molecular activity diff --git a/graphviz/molecular_activity_to_pathway_association.gv b/graphviz/molecular_activity_to_pathway_association.gv index a32882d6fa..f4e2df3211 100644 --- a/graphviz/molecular_activity_to_pathway_association.gv +++ b/graphviz/molecular_activity_to_pathway_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3016,283"]; + graph [bb="0,0,4748,283"]; node [label="\N"]; "molecular activity to pathway association" [height=0.5, label="molecular activity to pathway association", - pos="1551.4,265", + pos="2468.4,265", width=5.6509]; association [height=0.5, pos="62.394,178", width=1.7332]; "molecular activity to pathway association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1348.5,263.67 1040.8,262.29 470.76,256.01 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2265.6,263.37 1758.2,261.43 460.92,254.06 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "molecular activity to pathway association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1350.7,262.01 1069.6,258.52 572.67,249.6 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2266.3,262.74 1780.2,259.41 572.1,249.2 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular activity to pathway association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1353.2,260.91 1098,256.32 668.75,246.3 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,194.16 \ -324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2266.9,262.45 1800.5,258.58 673.05,247.44 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "molecular activity to pathway association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1352.1,261.35 1117.6,257.4 742.63,248.26 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2266.2,262.87 1816,259.96 757.96,250.87 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "molecular activity to pathway association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1350,262.2 1138.7,259.15 821.06,250.96 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2265.6,263.55 1833,262.07 847.02,255.77 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "molecular activity to pathway association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1353.6,260.74 1177.1,256.66 932.44,247.76 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2265.8,263.32 1859.5,261.42 972.23,254.38 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "molecular activity to pathway association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1356.5,259.77 1251.7,255.42 1120.5,246.66 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2264.9,264.29 1922.7,263.9 1245.8,259.17 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "molecular activity to pathway association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1369.7,256.85 1294.6,251.85 1206.9,243.37 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2264.9,264.32 1949,263.84 1355.1,258.82 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "molecular activity to pathway association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1397.7,253.16 1349.8,247.92 1297,240.23 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2265,264.24 1977.1,263.51 1465.4,257.97 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "molecular activity to pathway association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1457.5,248.97 1431.6,243.75 1403.6,237.12 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2265.8,263.31 2011.2,261.36 1588.7,254.27 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "molecular activity to pathway association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1506.2,247.43 1497.7,242.58 1489.5,236.51 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2271,260.63 2027.3,255.79 1637.1,245.59 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "molecular activity to pathway association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.7,247.07 1591.6,241.44 1602.5,235.06 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2270.1,260.97 2053.1,256.74 1733,247.41 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "molecular activity to pathway association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1719.1,254.71 1754.9,249.4 1792,241.29 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,202.83 \ -1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2279.4,258.27 2122.2,252.55 1922.2,242.65 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "molecular activity to pathway association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.17 1694.6,252.19 1717.9,250.38 1741.8,248.58 1764.4,247 1830.4,242.37 1999.9,253.38 2061.4,229 2069.3,225.85 2084,213.71 \ -2096.8,202.18", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2302.4,254.58 2226.4,248.79 2150,240.31 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "molecular activity to pathway association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1692.8,252.04 1716.7,250.22 1741.3,248.46 1764.4,247 1851,241.55 2071.8,255.63 2154.4,229 2166,225.25 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2290.5,256.25 2255.7,250.98 2226.2,242.51 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "molecular activity to pathway association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.49 1691.4,251.92 1715.7,250.08 1740.8,248.35 1764.4,247 1822.7,243.68 2235,250.26 2289.4,229 2297.1,225.97 2311.2,213.97 \ -2323.5,202.49", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2377.3,248.84 2357.5,243.66 2340.6,237.09 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,205 @@ digraph { width=1.0652]; "molecular activity to pathway association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.42 1690.5,251.83 1715.1,249.98 1740.5,248.27 1764.4,247 1801.9,245.01 2408.3,249.92 2439.4,229 2447.3,223.7 2452.4,\ -214.88 2455.6,206.11", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "molecular activity to pathway association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2541.5,248.12 2552.7,243.33 2563.5,237.1 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "molecular activity to pathway association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2625.6,253.54 2653.3,248.18 2681.3,240.35 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "molecular activity to pathway association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.51 2609.3,251.97 2714.1,242.87 2839.8,231.51 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "molecular activity to pathway association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2996.9,196.21 2611.6,252.19 2634.9,250.37 2658.8,248.58 2681.4,247 2714.6,244.68 2953.8,248.95 2980.4,229 2987.7,223.52 2992.1,\ +214.77 2994.7,206.12", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "molecular activity to pathway association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.1 2609.6,252.01 2633.5,250.18 2658.2,248.43 2681.4,247 2727.5,244.16 3055.9,251.2 3096.4,229 3106.1,223.65 3113.8,214.28 \ +3119.4,205.08", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "molecular activity to pathway association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.1 2607.8,251.86 2632.3,250.02 2657.6,248.3 2681.4,247 2715.3,245.15 3263,245.95 3292.4,229 3301.6,223.7 3308.4,214.47 \ +3313.3,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "molecular activity to pathway association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.18 2607,251.79 2631.7,249.93 2657.3,248.23 2681.4,247 2725.6,244.74 3439.3,249.9 3478.4,229 3488.2,223.75 3495.9,214.4 \ +3501.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "molecular activity to pathway association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.73 2606.4,251.76 2631.3,249.89 2657.1,248.2 2681.4,247 2734.3,244.39 3588.3,253.3 3635.4,229 3645.7,223.67 3653.9,213.99 \ +3659.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "molecular activity to pathway association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.77 2606.1,251.73 2631.1,249.86 2657,248.17 2681.4,247 2712,245.53 3757,242.67 3784.4,229 3795.1,223.66 3803.8,213.84 \ +3810.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "molecular activity to pathway association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2605.8,251.7 2630.9,249.83 2656.9,248.15 2681.4,247 2716.7,245.34 3922.6,244.54 3954.4,229 3965.3,223.69 3974.1,\ +213.87 3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "molecular activity to pathway association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2605.5,251.69 2630.7,249.82 2656.8,248.13 2681.4,247 2721.2,245.16 4080.6,248.34 4115.4,229 4124.9,223.75 4131.9,\ +214.39 4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "molecular activity to pathway association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.3,195.51 1690,251.79 1714.7,249.94 1740.3,248.23 1764.4,247 1786.5,245.87 2544,244.8 2559.4,229 2565.6,222.65 2565.4,213.61 \ -2562.9,204.95", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2605.5,251.67 2630.7,249.79 2656.8,248.12 2681.4,247 2703.5,245.99 4257.8,243.61 4274.4,229 4280.9,223.32 4283.4,\ +214.65 4284.1,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "molecular activity to pathway association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.84 1689.7,251.79 1714.5,249.93 1740.2,248.22 1764.4,247 1810.8,244.65 2558.7,247.48 2601.4,229 2613.8,223.64 2624.6,\ -213.54 2632.9,203.81", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2605.5,251.66 2630.7,249.79 2656.8,248.11 2681.4,247 2726.9,244.94 4276.5,244.21 4319.4,229 4334.6,223.59 4349,212.83 \ +4360.1,202.68", style=solid]; subject [height=0.5, - pos="2764.4,178", + pos="4496.4,178", width=1.2277]; "molecular activity to pathway association" -> subject [color=blue, label=subject, - lp="2747.4,221.5", - pos="e,2747.4,194.73 1689.4,251.77 1714.3,249.9 1740.1,248.2 1764.4,247 1815.8,244.45 2641.3,244.54 2690.4,229 2708.4,223.3 2726,211.71 \ -2739.5,201.13", + lp="4473.4,221.5", + pos="e,4477.7,194.32 2605.2,251.67 2630.5,249.79 2656.8,248.11 2681.4,247 2777.5,242.67 4320.8,255.25 4413.4,229 4433.6,223.28 4453.7,\ +211.29 4469.2,200.49", style=solid]; object [height=0.5, - pos="2807.4,91", + pos="4539.4,91", width=1.0832]; "molecular activity to pathway association" -> object [color=blue, label=object, - lp="2850.4,178", - pos="e,2820.8,108.09 1689.4,251.73 1714.3,249.87 1740.1,248.18 1764.4,247 1820.6,244.26 2724.6,248.5 2777.4,229 2819.9,213.31 2825.1,\ -186.96 2830.4,142 2831.2,135.38 2832.3,133.39 2830.4,127 2829.4,123.55 2827.9,120.13 2826.1,116.85", + lp="4583.4,178", + pos="e,4552.8,108.09 2605.2,251.66 2630.5,249.78 2656.7,248.1 2681.4,247 2732,244.74 4455.3,244.73 4503.4,229 4527.3,221.18 4535.3,216.87 \ +4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,116.85", style=solid]; predicate [height=0.5, - pos="2961.4,178", + pos="4693.4,178", width=1.5165]; "molecular activity to pathway association" -> predicate [color=blue, label=predicate, - lp="2934.4,221.5", - pos="e,2937.6,194.3 1689.1,251.73 1714.1,249.86 1740,248.17 1764.4,247 1885.8,241.16 2740.1,257.21 2858.4,229 2883.3,223.07 2909.1,210.47 \ -2928.7,199.41", + lp="4666.4,221.5", + pos="e,4669.6,194.35 2605.2,251.65 2630.5,249.77 2656.7,248.1 2681.4,247 2787.3,242.28 4487.1,253.25 4590.4,229 4615.3,223.15 4641.2,\ +210.56 4660.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1811.4,265", + pos="2728.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1942.4,265", + pos="2859.4,265", width=2.0762]; subject -> object [label=relation, - lp="2802.4,134.5", - pos="e,2789.5,107.23 2765.5,159.55 2766.7,149.57 2769.2,137.07 2774.4,127 2776.6,122.68 2779.5,118.52 2782.7,114.66"]; + lp="4534.4,134.5", + pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; relation [height=0.5, - pos="2752.4,18", + pos="4484.4,18", width=1.2999]; - subject -> relation [pos="e,2753.7,36.188 2763.1,159.79 2761,132.48 2757,78.994 2754.5,46.38", + subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", style=dotted]; "molecular activity to pathway association_subject" [color=blue, height=0.5, label="molecular activity", - pos="2129.4,265", + pos="3046.4,265", width=2.6178]; - object -> relation [pos="e,2765.2,35.54 2794.9,73.889 2788,64.939 2779.2,53.617 2771.4,43.584", + object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", style=dotted]; "molecular activity to pathway association_object" [color=blue, height=0.5, label=pathway, - pos="2291.4,265", + pos="3208.4,265", width=1.3902]; "molecular activity to pathway association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2437.4,265", + pos="3354.4,265", width=2.1665]; } diff --git a/graphviz/molecular_activity_to_pathway_association.svg b/graphviz/molecular_activity_to_pathway_association.svg index 3312ca81c4..b426010864 100644 --- a/graphviz/molecular_activity_to_pathway_association.svg +++ b/graphviz/molecular_activity_to_pathway_association.svg @@ -4,16 +4,16 @@ - + %3 - + molecular activity to pathway association - -molecular activity to pathway association + +molecular activity to pathway association @@ -24,9 +24,9 @@ molecular activity to pathway association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ molecular activity to pathway association->id - - -id + + +id @@ -50,9 +50,9 @@ molecular activity to pathway association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular activity to pathway association->name - - -name + + +name @@ -76,9 +76,9 @@ molecular activity to pathway association->description - - -description + + +description @@ -89,9 +89,9 @@ molecular activity to pathway association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ molecular activity to pathway association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ molecular activity to pathway association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ molecular activity to pathway association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ molecular activity to pathway association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ molecular activity to pathway association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ molecular activity to pathway association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ molecular activity to pathway association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ molecular activity to pathway association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ molecular activity to pathway association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ molecular activity to pathway association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ molecular activity to pathway association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +molecular activity to pathway association->subject category + + +subject category + + + +object category + +ontology class + + + +molecular activity to pathway association->object category + + +object category + + + +subject closure + +string + + + +molecular activity to pathway association->subject closure + + +subject closure + + + +object closure + +string + + + +molecular activity to pathway association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +molecular activity to pathway association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +molecular activity to pathway association->object category closure + + +object category closure + + + +subject namespace + +string + + + +molecular activity to pathway association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +molecular activity to pathway association->object namespace + + +object namespace + + + +subject label closure + +string + + + +molecular activity to pathway association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +molecular activity to pathway association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +molecular activity to pathway association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + molecular activity to pathway association->type - - -type + + +type - + category - -category + +category - + molecular activity to pathway association->category - - -category + + +category - + subject - -subject + +subject - + molecular activity to pathway association->subject - - -subject + + +subject - + object - -object + +object - + molecular activity to pathway association->object - - -object + + +object - + predicate - -predicate + +predicate - + molecular activity to pathway association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + molecular activity to pathway association_subject - -molecular activity + +molecular activity - + object->relation - - + + - + molecular activity to pathway association_object - -pathway + +pathway - + molecular activity to pathway association_predicate - -predicate type + +predicate type diff --git a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv index f4fa20a36b..9a67d67f2e 100644 --- a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv +++ b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4087.7,283"]; + graph [bb="0,0,5810.7,283"]; node [label="\N"]; "named thing associated with likelihood of named thing association" [height=0.5, label="named thing associated with likelihood of named thing association", - pos="1789.4,265", + pos="2706.4,265", width=8.8825]; association [height=0.5, pos="62.394,178", width=1.7332]; "named thing associated with likelihood of named thing association" -> association [label=is_a, - lp="277.39,221.5", - pos="e,102.69,191.82 1469.4,264.95 1092.1,264.61 487.71,259.1 263.39,229 211.04,221.98 152.59,206.55 112.28,194.68"]; + lp="279.39,221.5", + pos="e,102.71,191.81 2387.7,263.46 1773.9,261.84 469.9,255.3 265.39,229 212.35,222.18 153.11,206.64 112.39,194.69"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "named thing associated with likelihood of named thing association" -> id [color=blue, label=id, - lp="390.39,221.5", - pos="e,210.39,189.95 1471.5,262.96 1122.9,260.59 585.94,253.01 383.39,229 313.88,220.76 296.75,215.06 229.39,196 226.29,195.12 223.09,\ -194.15 219.9,193.12", + lp="394.39,221.5", + pos="e,210.38,189.97 2389.3,262.58 1800.5,259.44 580.49,250.42 387.39,229 316.09,221.09 298.47,215.35 229.39,196 226.29,195.13 223.09,\ +194.16 219.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -30,8 +30,7 @@ digraph { "named thing associated with likelihood of named thing association" -> iri [color=blue, label=iri, lp="490.39,221.5", - pos="e,315.34,190.07 1472.5,262.57 1148.2,259.83 666.47,251.91 482.39,229 415.95,220.73 400.01,213.58 335.39,196 332.03,195.08 328.56,\ -194.09 325.08,193.05", + pos="e,315.53,190.04 2389.2,262.61 1819.8,259.58 666.01,250.82 482.39,229 427.19,222.44 365.34,205.43 325.24,193.07", style=solid]; name [color=blue, height=0.5, @@ -41,7 +40,7 @@ digraph { "named thing associated with likelihood of named thing association" -> name [color=blue, label=name, lp="586.39,221.5", - pos="e,435.84,192.38 1469.6,264.43 1166.5,263.1 733.46,256.2 566.39,229 524.49,222.18 478.38,207.57 445.58,195.89", + pos="e,435.51,192.39 2387.2,263.66 1834.4,262.35 740.71,256.29 566.39,229 524.32,222.41 478.05,207.7 445.24,195.93", style=solid]; description [color=blue, height=0.5, @@ -51,7 +50,7 @@ digraph { "named thing associated with likelihood of named thing association" -> description [color=blue, label=description, lp="689.89,221.5", - pos="e,575.56,195.17 1475.8,261.41 1166,257.72 727.34,249.01 649.39,229 626.45,223.11 602.73,211.19 584.37,200.46", + pos="e,575.53,195.27 2390,262.36 1833.9,258.94 732.04,249.61 649.39,229 626.41,223.27 602.69,211.35 584.34,200.59", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,7 +60,7 @@ digraph { "named thing associated with likelihood of named thing association" -> "has attribute" [color=blue, label="has attribute", lp="808.39,221.5", - pos="e,711.75,195.36 1471.7,262.93 1194.6,260.4 826.96,252.55 761.39,229 745.72,223.37 730.79,212.44 719.21,202.23", + pos="e,711.72,195.45 2387.7,263.47 1855.5,261.85 836.5,255.3 761.39,229 745.67,223.49 730.74,212.58 719.17,202.35", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +70,7 @@ digraph { "named thing associated with likelihood of named thing association" -> subject [color=blue, label=subject, lp="902.39,221.5", - pos="e,845.03,196.18 1491.1,258.49 1235.4,252.83 903.94,242.9 876.39,229 865.76,223.63 857.01,214 850.44,204.6", + pos="e,844.99,196.26 2386.4,264.9 1879.6,265.33 942.71,261.66 876.39,229 865.7,223.74 856.95,214.11 850.39,204.71", style=solid]; object [color=blue, height=0.5, @@ -81,7 +80,8 @@ digraph { "named thing associated with likelihood of named thing association" -> object [color=blue, label=object, lp="973.39,178", - pos="e,931.67,109.1 1492.3,258.3 1267.1,250.96 990.03,234.19 951.39,196 931.42,176.26 929.29,142.8 930.78,119.18", + pos="e,931.68,109.09 2392,261.63 2012.4,257.93 1396.4,249.01 1167.4,229 1070.6,220.55 1020.4,264.31 951.39,196 931.43,176.25 929.3,142.79 \ +930.79,119.17", style=solid]; negated [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.2999]; "named thing associated with likelihood of named thing association" -> negated [color=blue, label=negated, - lp="1271.4,221.5", - pos="e,1085.8,190.35 1514.3,255.77 1427,250.66 1330.4,242.38 1242.4,229 1191.2,221.22 1134,205.22 1095.6,193.4", + lp="1276.4,221.5", + pos="e,1085.6,190.46 2387,264 2025.5,262.65 1459.4,256.06 1247.4,229 1194.1,222.2 1134.5,205.66 1095.1,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.1304]; "named thing associated with likelihood of named thing association" -> qualifiers [color=blue, label=qualifiers, - lp="1399.9,221.5", - pos="e,1233.3,193.25 1553.9,252.8 1492.6,247.62 1426.7,240.05 1366.4,229 1324.2,221.27 1277.5,207.56 1243.1,196.45", + lp="1416.9,221.5", + pos="e,1234.7,193.07 2387,263.96 2058.6,262.4 1569.6,255.47 1383.4,229 1335.6,222.2 1282.5,207.74 1244.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=1.7332]; "named thing associated with likelihood of named thing association" -> publications [color=blue, label=publications, - lp="1531.4,221.5", - pos="e,1382.2,193.34 1609.3,250.07 1568.9,245.03 1526.4,238.2 1487.4,229 1454.5,221.24 1418.6,208.09 1391.7,197.22", + lp="1564.4,221.5", + pos="e,1386.1,192.71 2387.3,263.72 2093.9,261.79 1680.9,254.4 1520.4,229 1477.3,222.18 1429.8,207.69 1395.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=2.0943]; "named thing associated with likelihood of named thing association" -> "has evidence" [color=blue, label="has evidence", - lp="1662.9,221.5", - pos="e,1535.3,194.68 1690.1,247.86 1665.7,242.82 1639.9,236.56 1616.4,229 1591.8,221.08 1565.4,209.32 1544.5,199.19", + lp="1718.9,221.5", + pos="e,1543.9,193.61 2390.4,262.18 2138,259.06 1805.4,250.8 1672.4,229 1631.5,222.3 1586.6,208.48 1553.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "named thing associated with likelihood of named thing association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1785.9,221.5", - pos="e,1708.8,196.34 1743.5,247.03 1735.2,242.25 1727.4,236.31 1721.4,229 1716.1,222.52 1712.8,214.16 1710.8,206.15", + lp="1873.9,221.5", + pos="e,1733.5,195.59 2408,258.48 2169.8,253.04 1866.6,243.44 1809.4,229 1785.9,223.07 1761.5,211.31 1742.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "named thing associated with likelihood of named thing association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1968.4,221.5", - pos="e,1908.7,195.19 1819.7,247.07 1829.6,241.44 1840.5,235.06 1850.4,229 1860.8,222.63 1862.8,220.1 1873.4,214 1881.8,209.16 1890.9,\ -204.28 1899.7,199.76", + lp="2045.4,221.5", + pos="e,1940.1,196.41 2406.4,258.75 2203,253.78 1968,244.69 1950.4,229 1944.1,223.34 1941.4,214.82 1940.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=3.015]; "named thing associated with likelihood of named thing association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2192.9,221.5", - pos="e,2131.7,194.43 1981.8,250.61 2009.7,245.47 2037.6,238.48 2063.4,229 2074.8,224.79 2075.5,219.55 2086.4,214 2097.7,208.22 2110.2,\ -202.83 2122.2,198.09", + lp="2253.9,221.5", + pos="e,2156.7,195.97 2438.5,255.16 2300.3,249.24 2158.1,240.44 2147.4,229 2140.4,221.54 2143.6,212.18 2150,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -162,8 +160,8 @@ digraph { width=1.5346]; "named thing associated with likelihood of named thing association" -> timepoint [color=blue, label=timepoint, - lp="2356.4,221.5", - pos="e,2342.5,195.15 2009.8,251.93 2141.3,244.22 2285.3,234.64 2299.4,229 2307.3,225.82 2322,213.68 2334.8,202.16", + lp="2409.4,221.5", + pos="e,2359.9,196.47 2500.1,251.23 2439.2,245.68 2385.6,238.29 2374.4,229 2367.6,223.41 2363.9,214.91 2361.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -172,9 +170,8 @@ digraph { width=1.0652]; "named thing associated with likelihood of named thing association" -> "original subject" [color=blue, label="original subject", - lp="2471.4,221.5", - pos="e,2449.3,192.7 2015,252.23 2182.4,243.29 2383.2,232.04 2392.4,229 2404,225.18 2405.1,220.57 2415.4,214 2423.6,208.79 2432.4,203.21 \ -2440.7,198.07", + lp="2508.4,221.5", + pos="e,2457.6,194.92 2501.4,251.17 2478.9,245.97 2460.9,238.82 2452.4,229 2446.1,221.83 2447.9,212.39 2452.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -183,9 +180,8 @@ digraph { width=1.5887]; "named thing associated with likelihood of named thing association" -> "original predicate" [color=blue, label="original predicate", - lp="2612.9,221.5", - pos="e,2568.8,195.47 2014.1,252.16 2049,250.38 2084.7,248.61 2118.4,247 2163.8,244.83 2485.1,245.78 2527.4,229 2535.1,225.93 2549.1,213.93 \ -2561.5,202.46", + lp="2635.9,221.5", + pos="e,2574.3,195.76 2611.1,247.72 2593.2,242.73 2578.2,236.52 2572.4,229 2567.1,222.16 2567.6,213.39 2570.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -194,72 +190,187 @@ digraph { width=1.0652]; "named thing associated with likelihood of named thing association" -> "original object" [color=blue, label="original object", - lp="2741.9,221.5", - pos="e,2696.6,196.41 2010.6,251.98 2046.6,250.19 2083.5,248.46 2118.4,247 2149.4,245.7 2651.6,246.4 2677.4,229 2685.3,223.68 2690.4,214.85 \ -2693.6,206.09", + lp="2754.9,221.5", + pos="e,2700.8,196.18 2705,246.8 2704,235.16 2702.7,219.55 2701.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2832.4,178", + width=2.1304]; + "named thing associated with likelihood of named thing association" -> "subject category" [color=blue, + label="subject category", + lp="2880.9,221.5", + pos="e,2828.6,196.4 2781.1,247.43 2791.8,242.73 2802,236.71 2810.4,229 2817.1,222.84 2821.9,214.24 2825.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3003.4,178", + width=2.1304]; + "named thing associated with likelihood of named thing association" -> "object category" [color=blue, + label="object category", + lp="3023.9,221.5", + pos="e,2988.6,195.73 2880.9,249.86 2902.8,244.76 2924.5,237.99 2944.4,229 2958,222.83 2971,212.54 2981.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3136.4,178", + width=1.0652]; + "named thing associated with likelihood of named thing association" -> "subject closure" [color=blue, + label="subject closure", + lp="3159.9,221.5", + pos="e,3124,195.51 2952.2,253.41 3007.8,248.23 3057.9,240.5 3083.4,229 3096.3,223.16 3108.1,212.86 3117.2,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3236.4,178", + width=1.0652]; + "named thing associated with likelihood of named thing association" -> "object closure" [color=blue, + label="object closure", + lp="3280.4,221.5", + pos="e,3234.9,196.19 2923.8,251.78 3060.4,243.67 3212.2,233.69 3218.4,229 3225.7,223.49 3230,214.74 3232.6,206.09", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3369.4,178", + width=2.1304]; + "named thing associated with likelihood of named thing association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3437.9,221.5", + pos="e,3362.3,196.05 2929.8,252.11 3109.3,242.46 3332.1,230.27 3334.4,229 3344.1,223.59 3351.8,214.21 3357.4,205.02", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3561.4,178", + width=2.1304]; + "named thing associated with likelihood of named thing association" -> "object category closure" [color=blue, + label="object category closure", + lp="3628.9,221.5", + pos="e,3555.4,196.09 2928.9,252.04 2964.5,250.26 3001,248.52 3035.4,247 3062.8,245.79 3505.5,242.62 3529.4,229 3538.8,223.63 3545.9,214.26 \ +3550.9,205.06", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3751.4,178", + width=1.0652]; + "named thing associated with likelihood of named thing association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3801.4,221.5", + pos="e,3744.4,196.17 2925.8,251.89 2962.4,250.09 3000,248.38 3035.4,247 3073.2,245.52 3683.1,246.92 3716.4,229 3726.2,223.73 3733.8,214.37 \ +3739.5,205.17", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3910.4,178", + width=1.0652]; + "named thing associated with likelihood of named thing association" -> "object namespace" [color=blue, + label="object namespace", + lp="3954.4,221.5", + pos="e,3903,195.72 2924.5,251.81 2961.5,250 2999.5,248.31 3035.4,247 3081.9,245.3 3832,250.4 3873.4,229 3883.7,223.66 3891.9,213.97 3897.9,\ +204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4061.4,178", + width=1.0652]; + "named thing associated with likelihood of named thing association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4114.4,221.5", + pos="e,4053.4,195.76 2923.6,251.75 2960.9,249.94 2999.2,248.26 3035.4,247 3090.2,245.08 3973.3,253.51 4022.4,229 4033.1,223.65 4041.7,\ +213.83 4048.2,204.29", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4232.4,178", + width=1.0652]; + "named thing associated with likelihood of named thing association" -> "object label closure" [color=blue, + label="object label closure", + lp="4279.9,221.5", + pos="e,4224.1,195.78 2922.7,251.71 2960.3,249.89 2999,248.22 3035.4,247 3067.5,245.92 4163.5,243.15 4192.4,229 4203.2,223.68 4212.1,213.86 \ +4218.7,204.32", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4376.4,178", + width=2.347]; + "named thing associated with likelihood of named thing association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4435.9,221.5", + pos="e,4373.4,196 2921.8,251.69 2959.7,249.87 2998.7,248.2 3035.4,247 3072,245.81 4322.7,248.96 4353.4,229 4361.5,223.7 4366.8,214.72 \ +4370.3,205.82", style=solid]; type [height=0.5, - pos="2787.4,178", + pos="4510.4,178", width=0.86659]; "named thing associated with likelihood of named thing association" -> type [color=blue, label=type, - lp="2819.4,221.5", - pos="e,2797.2,195.5 2008.8,251.89 2045.4,250.1 2083,248.38 2118.4,247 2137.2,246.26 2784.2,242.52 2797.4,229 2803.6,222.64 2803.4,213.59 \ -2800.9,204.94", + lp="4532.4,221.5", + pos="e,4515.5,196.18 2921.4,251.67 2959.3,249.84 2998.5,248.18 3035.4,247 3055.9,246.35 4494.9,243.42 4509.4,229 4515.4,223.09 4517,214.51 \ +4516.6,206.12", style=solid]; category [height=0.5, - pos="2888.4,178", + pos="4611.4,178", width=1.4263]; "named thing associated with likelihood of named thing association" -> category [color=blue, label=category, - lp="2892.9,221.5", - pos="e,2877.3,195.82 2008.4,251.87 2045.1,250.07 2082.8,248.36 2118.4,247 2158.4,245.47 2802.7,244.98 2839.4,229 2851.8,223.62 2862.6,\ -213.52 2870.9,203.79", + lp="4609.9,221.5", + pos="e,4597.8,195.45 2921.4,251.66 2959.3,249.83 2998.5,248.17 3035.4,247 3077.5,245.66 4512.9,243.74 4552.4,229 4567,223.56 4580.4,212.8 \ +4590.8,202.65", style=solid]; predicate [height=0.5, - pos="3012.4,178", + pos="4735.4,178", width=1.5165]; "named thing associated with likelihood of named thing association" -> predicate [color=blue, label=predicate, - lp="2997.4,221.5", - pos="e,2992.4,194.97 2007.5,251.83 2044.5,250.02 2082.5,248.32 2118.4,247 2208.4,243.68 2841.9,253.84 2928.4,229 2948.3,223.28 2968.3,\ -211.65 2983.8,201.05", + lp="4716.4,221.5", + pos="e,4714.2,194.81 2921.4,251.64 2959.3,249.81 2998.5,248.16 3035.4,247 3124.8,244.19 4558.9,251.92 4645.4,229 4666.8,223.32 4688.6,\ +211.41 4705.4,200.63", style=solid]; "subject aspect qualifier" [height=0.5, - pos="3204.4,178", + pos="4927.4,178", width=3.3039]; "named thing associated with likelihood of named thing association" -> "subject aspect qualifier" [color=blue, label="subject aspect qualifier", - lp="3185.9,221.5", - pos="e,3162.4,194.85 2007,251.77 2044.2,249.96 2082.4,248.28 2118.4,247 2322.1,239.74 2834,260.19 3035.4,229 3075.7,222.76 3119.9,209.45 \ -3152.9,198.14", + lp="4905.9,221.5", + pos="e,4884.7,194.84 2920.9,251.64 2959,249.81 2998.4,248.15 3035.4,247 3226.3,241.07 4565.4,256.77 4754.4,229 4795.8,222.92 4841.2,209.54 \ +4875.1,198.15", style=solid]; "subject context qualifier" [height=0.5, - pos="3464.4,178", + pos="5187.4,178", width=3.4303]; "named thing associated with likelihood of named thing association" -> "subject context qualifier" [color=blue, label="subject context qualifier", - lp="3435.4,221.5", - pos="e,3417.2,194.76 2005.7,251.71 2043.3,249.89 2082,248.23 2118.4,247 2246.7,242.69 3146.2,246.38 3273.4,229 3319.2,222.74 3369.8,209.18 \ -3407.4,197.77", + lp="5156.4,221.5", + pos="e,5139.8,194.73 2920.5,251.62 2958.7,249.78 2998.2,248.13 3035.4,247 3252.9,240.39 4777.7,257.36 4993.4,229 5040.1,222.86 5091.7,\ +209.23 5129.9,197.75", style=solid]; "object aspect qualifier" [height=0.5, - pos="3719.4,178", + pos="5442.4,178", width=3.1594]; "named thing associated with likelihood of named thing association" -> "object aspect qualifier" [color=blue, label="object aspect qualifier", - lp="3681.9,221.5", - pos="e,3672.8,194.44 2004.8,251.67 2042.7,249.84 2081.7,248.18 2118.4,247 2274.8,241.96 3371.3,249.77 3526.4,229 3573.2,222.74 3624.8,\ -208.97 3663,197.46", + lp="5402.9,221.5", + pos="e,5395.3,194.5 2920.5,251.59 2958.7,249.75 2998.2,248.11 3035.4,247 3158.2,243.33 5125.5,244.88 5247.4,229 5294.6,222.84 5346.9,\ +209.07 5385.4,197.53", style=solid]; "object context qualifier" [height=0.5, - pos="3969.4,178", + pos="5692.4,178", width=3.2858]; "named thing associated with likelihood of named thing association" -> "object context qualifier" [color=blue, label="object context qualifier", - lp="3927.4,221.5", - pos="e,3920.1,194.46 2003.9,251.65 2042,249.82 2081.4,248.16 2118.4,247 2301.3,241.28 3583.8,251.93 3765.4,229 3815,222.73 3870,208.82 \ -3910.4,197.26", + lp="5649.4,221.5", + pos="e,5643,194.38 2920,251.58 2958.4,249.74 2998.1,248.1 3035.4,247 3171.5,242.99 5351.2,245.67 5486.4,229 5536.7,222.8 5592.4,208.81 \ +5633.3,197.2", style=solid]; subject -> object [label=relation, lp="900.39,134.5", @@ -274,36 +385,36 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2165.4,265", + pos="3082.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2296.4,265", + pos="3213.4,265", width=2.0762]; "named thing associated with likelihood of named thing association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2467.4,265", + pos="3384.4,265", width=2.1665]; "named thing associated with likelihood of named thing association_subject aspect qualifier" [color=blue, height=0.5, label=string, - pos="2601.4,265", + pos="3518.4,265", width=1.0652]; "named thing associated with likelihood of named thing association_subject context qualifier" [color=blue, height=0.5, label="ontology class", - pos="2734.4,265", + pos="3651.4,265", width=2.1304]; "named thing associated with likelihood of named thing association_object aspect qualifier" [color=blue, height=0.5, label=string, - pos="2867.4,265", + pos="3784.4,265", width=1.0652]; "named thing associated with likelihood of named thing association_object context qualifier" [color=blue, height=0.5, label="ontology class", - pos="3000.4,265", + pos="3917.4,265", width=2.1304]; } diff --git a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg index 978b69c9c1..1203f0fea3 100644 --- a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg +++ b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg @@ -4,16 +4,16 @@ - + %3 - + named thing associated with likelihood of named thing association - -named thing associated with likelihood of named thing association + +named thing associated with likelihood of named thing association @@ -24,9 +24,9 @@ named thing associated with likelihood of named thing association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ named thing associated with likelihood of named thing association->id - - -id + + +id @@ -50,8 +50,8 @@ named thing associated with likelihood of named thing association->iri - - + + iri @@ -63,8 +63,8 @@ named thing associated with likelihood of named thing association->name - - + + name @@ -76,8 +76,8 @@ named thing associated with likelihood of named thing association->description - - + + description @@ -89,8 +89,8 @@ named thing associated with likelihood of named thing association->has attribute - - + + has attribute @@ -102,8 +102,8 @@ named thing associated with likelihood of named thing association->subject - - + + subject @@ -115,8 +115,8 @@ named thing associated with likelihood of named thing association->object - - + + object @@ -128,9 +128,9 @@ named thing associated with likelihood of named thing association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ named thing associated with likelihood of named thing association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ named thing associated with likelihood of named thing association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ named thing associated with likelihood of named thing association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ named thing associated with likelihood of named thing association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ named thing associated with likelihood of named thing association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ named thing associated with likelihood of named thing association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ named thing associated with likelihood of named thing association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ named thing associated with likelihood of named thing association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ named thing associated with likelihood of named thing association->original predicate - - -original predicate + + +original predicate @@ -258,167 +258,310 @@ named thing associated with likelihood of named thing association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +named thing associated with likelihood of named thing association->subject category + + +subject category + + + +object category + +ontology class + + + +named thing associated with likelihood of named thing association->object category + + +object category + + + +subject closure + +string + + + +named thing associated with likelihood of named thing association->subject closure + + +subject closure + + + +object closure + +string + + + +named thing associated with likelihood of named thing association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +named thing associated with likelihood of named thing association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +named thing associated with likelihood of named thing association->object category closure + + +object category closure + + + +subject namespace + +string + + + +named thing associated with likelihood of named thing association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +named thing associated with likelihood of named thing association->object namespace + + +object namespace + + + +subject label closure + +string + + + +named thing associated with likelihood of named thing association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +named thing associated with likelihood of named thing association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +named thing associated with likelihood of named thing association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + named thing associated with likelihood of named thing association->type - - -type + + +type - + category - -category + +category - + named thing associated with likelihood of named thing association->category - - -category + + +category - + predicate - -predicate + +predicate - + named thing associated with likelihood of named thing association->predicate - - -predicate + + +predicate - + subject aspect qualifier - -subject aspect qualifier + +subject aspect qualifier - + named thing associated with likelihood of named thing association->subject aspect qualifier - - -subject aspect qualifier + + +subject aspect qualifier - + subject context qualifier - -subject context qualifier + +subject context qualifier - + named thing associated with likelihood of named thing association->subject context qualifier - - -subject context qualifier + + +subject context qualifier - + object aspect qualifier - -object aspect qualifier + +object aspect qualifier - + named thing associated with likelihood of named thing association->object aspect qualifier - - -object aspect qualifier + + +object aspect qualifier - + object context qualifier - -object context qualifier + +object context qualifier - + named thing associated with likelihood of named thing association->object context qualifier - - -object context qualifier + + +object context qualifier - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type - + named thing associated with likelihood of named thing association_predicate - -predicate type + +predicate type - + named thing associated with likelihood of named thing association_subject aspect qualifier - -string + +string - + named thing associated with likelihood of named thing association_subject context qualifier - -ontology class + +ontology class - + named thing associated with likelihood of named thing association_object aspect qualifier - -string + +string - + named thing associated with likelihood of named thing association_object context qualifier - -ontology class + +ontology class diff --git a/graphviz/organism_taxon_to_environment_association.gv b/graphviz/organism_taxon_to_environment_association.gv index 59100da98d..e901318588 100644 --- a/graphviz/organism_taxon_to_environment_association.gv +++ b/graphviz/organism_taxon_to_environment_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3393,283"]; + graph [bb="0,0,5125,283"]; node [label="\N"]; "organism taxon to environment association" [height=0.5, label="organism taxon to environment association", - pos="1846.4,265", + pos="2770.4,265", width=5.8856]; association [height=0.5, pos="62.394,178", width=1.7332]; "organism taxon to environment association" -> association [label=is_a, - lp="508.39,221.5", - pos="e,106.89,190.69 1636,262.8 1370,260.31 897.85,252.64 494.39,229 333.56,219.58 292.37,222.16 133.39,196 128,195.11 122.41,194.04 \ -116.84,192.87"]; + lp="498.39,221.5", + pos="e,106.89,190.67 2559.8,262.89 2073.6,259.99 884.19,250.82 484.39,229 327.94,220.46 287.97,221.64 133.39,196 128,195.11 122.41,194.03 \ +116.84,192.86"]; "organism taxon to entity association" [height=0.5, pos="322.39,178", width=5.0009]; "organism taxon to environment association" -> "organism taxon to entity association" [label=uses, - lp="656.89,221.5", - pos="e,401.11,194.23 1639.4,261.17 1347,256.62 827.91,246.39 640.39,229 562.48,221.77 474.67,207.5 411.1,196.04"]; + lp="654.89,221.5", + pos="e,399.61,194.33 2558.4,264.31 2095.5,264.36 1006.3,260.96 638.39,229 560.53,222.23 472.78,207.8 409.55,196.17"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "organism taxon to environment association" -> id [color=blue, label=id, - lp="777.39,221.5", - pos="e,587.37,190.01 1638.8,261.35 1374.4,257.25 932.56,247.82 770.39,229 696.54,220.43 678.06,215.79 606.39,196 603.28,195.14 600.08,\ -194.18 596.89,193.17", + lp="773.39,221.5", + pos="e,587.38,189.98 2560.3,262.54 2082.1,258.91 940.62,248.32 766.39,229 694.23,221 676.34,215.5 606.39,196 603.29,195.13 600.09,194.17 \ +596.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "organism taxon to environment association" -> iri [color=blue, label=iri, - lp="896.39,221.5", - pos="e,692.01,190.17 1642.3,260.11 1405.3,254.96 1029,244.66 888.39,229 809.3,220.19 789.55,215.53 712.39,196 708.96,195.13 705.43,194.16 \ -701.9,193.14", + lp="886.39,221.5", + pos="e,692.3,190.2 2558.5,264.82 2135.1,265.68 1198.1,263.46 878.39,229 803.61,220.94 785.22,214.85 712.39,196 709.02,195.13 705.54,194.16 \ +702.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "organism taxon to environment association" -> name [color=blue, label=name, - lp="1000.4,221.5", - pos="e,817.4,191.21 1641.5,260.39 1426.6,255.76 1103.1,246.2 980.39,229 927.18,221.54 867.61,205.87 827.04,194.05", + lp="993.39,221.5", + pos="e,816.35,191.53 2560.3,262.63 2119.6,259.37 1126.6,249.8 973.39,229 922.26,222.06 865.25,206.49 826.14,194.56", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "organism taxon to environment association" -> description [color=blue, label=description, - lp="1119.9,221.5", - pos="e,964.28,193.99 1639.9,260.93 1450,256.95 1182.8,248.1 1079.4,229 1043,222.28 1003.4,208.92 973.88,197.7", + lp="1113.9,221.5", + pos="e,962.45,194.13 2559.1,263.31 2136.5,261.4 1215.7,254.35 1073.4,229 1038.3,222.75 1000.3,209.39 972.04,198.05", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "organism taxon to environment association" -> "has attribute" [color=blue, label="has attribute", - lp="1263.4,221.5", - pos="e,1104.2,192.62 1646.7,258.98 1493.7,254 1295.8,244.77 1216.4,229 1180.7,221.92 1141.9,207.92 1113.7,196.52", + lp="1259.4,221.5", + pos="e,1103,192.81 2559.8,263.04 2164.8,260.68 1341,252.92 1212.4,229 1177.4,222.5 1139.6,208.37 1112.2,196.79", style=solid]; negated [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.2999]; "organism taxon to environment association" -> negated [color=blue, label=negated, - lp="1412.4,221.5", - pos="e,1225.2,190.23 1658.6,256.61 1574.1,251.54 1473.4,243.07 1383.4,229 1331.8,220.93 1273.9,204.98 1235.1,193.26", + lp="1414.4,221.5", + pos="e,1224.4,190.44 2558.8,263.98 2228.5,263.06 1605.6,257.43 1385.4,229 1332.5,222.17 1273.3,205.69 1234.2,193.51", style=solid]; qualifiers [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1304]; "organism taxon to environment association" -> qualifiers [color=blue, label=qualifiers, - lp="1542.9,221.5", - pos="e,1373.7,193.09 1687.4,253.1 1630.9,247.75 1567,240 1509.4,229 1466.3,220.77 1418.5,207.08 1383.3,196.11", + lp="1553.9,221.5", + pos="e,1373.6,193.17 2558.6,263.96 2255.8,262.9 1714.3,256.97 1520.4,229 1473.2,222.19 1420.9,207.8 1383.3,196.2", style=solid]; publications [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.7332]; "organism taxon to environment association" -> publications [color=blue, label=publications, - lp="1669.4,221.5", - pos="e,1521.9,193.28 1730.3,249.91 1696.2,244.62 1659.1,237.72 1625.4,229 1593.2,220.66 1558,207.71 1531.3,197.08", + lp="1700.4,221.5", + pos="e,1524.5,192.69 2558.9,263.84 2285.4,262.5 1824,256.11 1656.4,229 1614,222.15 1567.3,207.66 1533.9,196.04", style=solid]; "has evidence" [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.0943]; "organism taxon to environment association" -> "has evidence" [color=blue, label="has evidence", - lp="1795.9,221.5", - pos="e,1675.3,194.69 1797.7,247.48 1782.1,241.92 1764.9,235.48 1749.4,229 1727.6,219.91 1703.8,208.7 1684.4,199.2", + lp="1853.9,221.5", + pos="e,1682.2,193.7 2560.1,262.76 2321.3,260.21 1946.7,252.48 1807.4,229 1767.6,222.29 1723.9,208.54 1691.8,197.15", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=3.015]; "organism taxon to environment association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1910.9,221.5", - pos="e,1846.4,196.18 1846.4,246.8 1846.4,235.16 1846.4,219.55 1846.4,206.24", + lp="2006.9,221.5", + pos="e,1870.8,195.57 2566.6,260.01 2340.9,254.86 2000.9,244.65 1942.4,229 1920.3,223.09 1897.5,211.49 1879.7,200.95", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -127,8 +127,8 @@ digraph { width=3.015]; "organism taxon to environment association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2104.4,221.5", - pos="e,2049.1,195.23 1917.6,248.04 1937.8,242.76 1959.7,236.33 1979.4,229 1985.7,226.64 2014.6,212.46 2040,199.8", + lp="2176.4,221.5", + pos="e,2076,196.02 2565.3,260.39 2368.3,255.88 2098.1,246.54 2081.4,229 2075.7,222.98 2074.2,214.49 2074.7,206.2", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -137,9 +137,8 @@ digraph { width=3.015]; "organism taxon to environment association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2331.9,221.5", - pos="e,2270.7,194.43 1998.5,252.43 2086.1,245.16 2182.8,235.9 2202.4,229 2213.9,224.95 2214.5,219.55 2225.4,214 2236.7,208.22 2249.2,\ -202.83 2261.2,198.09", + lp="2384.9,221.5", + pos="e,2291.1,195.65 2560.9,262.19 2436.1,258.87 2298.3,250.32 2278.4,229 2270.8,220.83 2275.3,211.21 2283.5,202.59", style=solid]; timepoint [color=blue, height=0.5, @@ -148,9 +147,8 @@ digraph { width=1.5346]; "organism taxon to environment association" -> timepoint [color=blue, label=timepoint, - lp="2495.4,221.5", - pos="e,2481.5,195.2 1994.1,252.06 2018.5,250.25 2043.7,248.49 2067.4,247 2108.6,244.42 2399.9,243.99 2438.4,229 2446.3,225.9 2461,213.76 \ -2473.8,202.22", + lp="2536.4,221.5", + pos="e,2494.4,195.96 2582.3,256.7 2545.5,251.41 2514.3,242.82 2501.4,229 2495.7,222.92 2493.9,214.4 2493.8,206.12", style=solid]; "original subject" [color=blue, height=0.5, @@ -159,9 +157,8 @@ digraph { width=1.0652]; "organism taxon to environment association" -> "original subject" [color=blue, label="original subject", - lp="2610.4,221.5", - pos="e,2588.3,192.7 1992.6,251.97 2017.5,250.14 2043.2,248.4 2067.4,247 2118.9,244.02 2482.2,244.66 2531.4,229 2543,225.3 2544.1,220.57 \ -2554.4,214 2562.6,208.79 2571.4,203.21 2579.7,198.07", + lp="2634.4,221.5", + pos="e,2590.9,193.67 2632.3,251.29 2607.5,246.17 2586.8,239.02 2578.4,229 2571.2,220.34 2576,209.96 2583.8,200.9", style=solid]; "original predicate" [color=blue, height=0.5, @@ -170,9 +167,8 @@ digraph { width=1.5887]; "organism taxon to environment association" -> "original predicate" [color=blue, label="original predicate", - lp="2751.9,221.5", - pos="e,2707.8,195.5 1991.7,251.85 2016.9,250.02 2042.9,248.31 2067.4,247 2133.9,243.45 2604.3,253.12 2666.4,229 2674.1,225.99 2688.2,\ -213.99 2700.5,202.5", + lp="2759.9,221.5", + pos="e,2705.7,195.47 2716.2,247.44 2708.3,242.71 2701.3,236.68 2696.4,229 2691.2,220.8 2694,211.6 2699.5,203.34", style=solid]; "original object" [color=blue, height=0.5, @@ -181,88 +177,205 @@ digraph { width=1.0652]; "organism taxon to environment association" -> "original object" [color=blue, label="original object", - lp="2880.9,221.5", - pos="e,2835.6,196.43 1990.8,251.79 2016.3,249.95 2042.6,248.25 2067.4,247 2109,244.9 2781.8,252.16 2816.4,229 2824.3,223.71 2829.4,214.89 \ -2832.6,206.12", + lp="2882.9,221.5", + pos="e,2836.3,196.07 2803.6,247.16 2811,242.15 2818.1,236.08 2823.4,229 2828.4,222.25 2831.8,213.82 2834,205.82", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2971.4,178", + width=2.1304]; + "organism taxon to environment association" -> "subject category" [color=blue, + label="subject category", + lp="3012.9,221.5", + pos="e,2964.4,195.94 2893,250.31 2909.1,245.19 2924.7,238.29 2938.4,229 2947.2,223.02 2954.3,213.82 2959.5,204.93", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3142.4,178", + width=2.1304]; + "organism taxon to environment association" -> "object category" [color=blue, + label="object category", + lp="3157.9,221.5", + pos="e,3125.8,195.64 2931.3,253.28 2990.4,247.72 3049.5,239.79 3076.4,229 3091.7,222.87 3106.5,212.22 3118.2,202.31", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3275.4,178", + width=1.0652]; + "organism taxon to environment association" -> "subject closure" [color=blue, + label="subject closure", + lp="3295.9,221.5", + pos="e,3262,195.11 2921.3,252.32 3050.7,242.28 3216.5,229.36 3217.4,229 3231.5,223.13 3244.6,212.48 3254.8,202.51", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3375.4,178", + width=1.0652]; + "organism taxon to environment association" -> "object closure" [color=blue, + label="object closure", + lp="3416.4,221.5", + pos="e,3372.9,196.32 2918.1,252.08 2942.5,250.27 2967.7,248.5 2991.4,247 3031.7,244.45 3321.3,252.18 3354.4,229 3362.1,223.58 3367,214.74 \ +3370.1,205.98", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3508.4,178", + width=2.1304]; + "organism taxon to environment association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3574.9,221.5", + pos="e,3500.4,196.16 2916.6,251.94 2941.5,250.12 2967.2,248.39 2991.4,247 3044.6,243.96 3423.1,253.56 3470.4,229 3480.7,223.67 3488.9,\ +214.17 3495.1,204.87", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3700.4,178", + width=2.1304]; + "organism taxon to environment association" -> "object category closure" [color=blue, + label="object category closure", + lp="3765.9,221.5", + pos="e,3693.7,196.15 2915.1,251.83 2940.5,249.99 2966.7,248.28 2991.4,247 3028.9,245.06 3633.5,246.99 3666.4,229 3676.1,223.71 3683.5,\ +214.35 3689,205.15", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3890.4,178", + width=1.0652]; + "organism taxon to environment association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3938.4,221.5", + pos="e,3883,195.72 2914.2,251.77 2939.9,249.92 2966.4,248.22 2991.4,247 3039.2,244.66 3810.8,251 3853.4,229 3863.7,223.66 3871.9,213.98 \ +3877.9,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4049.4,178", + width=1.0652]; + "organism taxon to environment association" -> "object namespace" [color=blue, + label="object namespace", + lp="4092.4,221.5", + pos="e,4041.4,195.76 2913.9,251.72 2939.7,249.87 2966.3,248.19 2991.4,247 3048,244.33 3959.7,254.29 4010.4,229 4021.1,223.65 4029.7,213.83 \ +4036.2,204.3", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4200.4,178", + width=1.0652]; + "organism taxon to environment association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4252.4,221.5", + pos="e,4192.1,195.78 2913.6,251.7 2939.5,249.84 2966.2,248.16 2991.4,247 3023.8,245.5 4131.2,243.29 4160.4,229 4171.2,223.68 4180.1,213.86 \ +4186.7,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4371.4,178", + width=1.0652]; + "organism taxon to environment association" -> "object label closure" [color=blue, + label="object label closure", + lp="4419.9,221.5", + pos="e,4362.8,195.8 2913.3,251.68 2939.2,249.82 2966.1,248.14 2991.4,247 3028.6,245.32 4296.9,245.14 4330.4,229 4341.4,223.71 4350.4,\ +213.89 4357.2,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4524.4,178", + width=2.347]; + "organism taxon to environment association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4577.9,221.5", + pos="e,4518.7,196.17 2913,251.67 2939,249.8 2966,248.13 2991.4,247 3033.1,245.15 4457.1,249.51 4493.4,229 4502.6,223.78 4509.5,214.56 \ +4514.4,205.45", style=solid]; type [height=0.5, - pos="2926.4,178", + pos="4658.4,178", width=0.86659]; "organism taxon to environment association" -> type [color=blue, label=type, - lp="2958.4,221.5", - pos="e,2936.3,195.51 1990.2,251.77 2015.9,249.91 2042.4,248.22 2067.4,247 2091.5,245.82 2919.5,246.25 2936.4,229 2942.6,222.66 2942.4,\ -213.62 2939.9,204.96", + lp="4676.4,221.5", + pos="e,4661.1,195.99 2913,251.65 2939,249.78 2966,248.11 2991.4,247 3014.4,245.99 4634.1,244.23 4651.4,229 4657.9,223.32 4660.4,214.65 \ +4661.1,206.12", style=solid]; category [height=0.5, - pos="3027.4,178", + pos="4759.4,178", width=1.4263]; "organism taxon to environment association" -> category [color=blue, label=category, - lp="3031.9,221.5", - pos="e,3016.3,195.84 1990.2,251.75 2015.9,249.9 2042.4,248.21 2067.4,247 2118,244.56 2931.9,249.07 2978.4,229 2990.8,223.65 3001.6,213.55 \ -3009.9,203.82", + lp="4754.9,221.5", + pos="e,4744.7,195.48 2912.7,251.66 2938.8,249.79 2965.9,248.11 2991.4,247 3038.7,244.93 4651.8,244.83 4696.4,229 4711.6,223.59 4726,212.84 \ +4737.1,202.68", style=solid]; subject [height=0.5, - pos="3141.4,178", + pos="4873.4,178", width=1.2277]; "organism taxon to environment association" -> subject [color=blue, label=subject, - lp="3124.4,221.5", - pos="e,3124.4,194.74 1989.9,251.73 2015.7,249.88 2042.3,248.19 2067.4,247 2122.9,244.37 3014.4,245.74 3067.4,229 3085.4,223.31 3103,211.73 \ -3116.5,201.14", + lp="4850.4,221.5", + pos="e,4854.7,194.32 2912.7,251.65 2938.8,249.78 2965.9,248.11 2991.4,247 3091.2,242.66 4694.2,256.25 4790.4,229 4810.6,223.29 4830.7,\ +211.3 4846.2,200.49", style=solid]; object [height=0.5, - pos="3184.4,91", + pos="4916.4,91", width=1.0832]; "organism taxon to environment association" -> object [color=blue, label=object, - lp="3227.4,178", - pos="e,3197.8,108.09 1989.6,251.72 2015.5,249.86 2042.2,248.18 2067.4,247 2127.7,244.18 3097.7,249.89 3154.4,229 3196.9,213.34 3202.1,\ -186.96 3207.4,142 3208.2,135.38 3209.3,133.39 3207.4,127 3206.4,123.55 3204.9,120.13 3203.1,116.85", + lp="4960.4,178", + pos="e,4929.8,108.09 2912.7,251.64 2938.8,249.77 2965.9,248.1 2991.4,247 3043.8,244.74 4830.5,245.3 4880.4,229 4904.3,221.18 4912.3,216.87 \ +4926.4,196 4940.2,175.52 4936.5,166.51 4939.4,142 4940.2,135.38 4941.3,133.39 4939.4,127 4938.4,123.55 4936.9,120.13 4935.1,116.85", style=solid]; predicate [height=0.5, - pos="3338.4,178", + pos="5070.4,178", width=1.5165]; "organism taxon to environment association" -> predicate [color=blue, label=predicate, - lp="3311.4,221.5", - pos="e,3314.6,194.31 1989.6,251.7 2015.5,249.84 2042.2,248.16 2067.4,247 2132.2,244.01 3172.3,244.03 3235.4,229 3260.3,223.08 3286.1,\ -210.49 3305.7,199.42", + lp="5043.4,221.5", + pos="e,5046.6,194.36 2912.7,251.63 2938.8,249.76 2965.9,248.09 2991.4,247 3101.1,242.29 4860.5,254.08 4967.4,229 4992.3,223.16 5018.2,\ +210.56 5037.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2114.4,265", + pos="3038.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2245.4,265", + pos="3169.4,265", width=2.0762]; subject -> object [label=relation, - lp="3179.4,134.5", - pos="e,3166.5,107.23 3142.5,159.55 3143.7,149.57 3146.2,137.07 3151.4,127 3153.6,122.68 3156.5,118.52 3159.7,114.66"]; + lp="4911.4,134.5", + pos="e,4898.5,107.23 4874.5,159.55 4875.7,149.57 4878.2,137.07 4883.4,127 4885.6,122.68 4888.5,118.52 4891.7,114.66"]; relation [height=0.5, - pos="3129.4,18", + pos="4861.4,18", width=1.2999]; - subject -> relation [pos="e,3130.7,36.188 3140.1,159.79 3138,132.48 3134,78.994 3131.5,46.38", + subject -> relation [pos="e,4862.7,36.188 4872.1,159.79 4870,132.48 4866,78.994 4863.5,46.38", style=dotted]; "organism taxon to environment association_subject" [color=blue, height=0.5, label="organism taxon", - pos="2421.4,265", + pos="3345.4,265", width=2.3109]; - object -> relation [pos="e,3142.2,35.54 3171.9,73.889 3165,64.939 3156.2,53.617 3148.4,43.584", + object -> relation [pos="e,4874.2,35.54 4903.9,73.889 4897,64.939 4888.2,53.617 4880.4,43.584", style=dotted]; "organism taxon to environment association_object" [color=blue, height=0.5, label="named thing", - pos="2592.4,265", + pos="3516.4,265", width=1.9318]; "organism taxon to environment association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2758.4,265", + pos="3682.4,265", width=2.1665]; } diff --git a/graphviz/organism_taxon_to_environment_association.svg b/graphviz/organism_taxon_to_environment_association.svg index d2817d997b..31d30146d2 100644 --- a/graphviz/organism_taxon_to_environment_association.svg +++ b/graphviz/organism_taxon_to_environment_association.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to environment association - -organism taxon to environment association + +organism taxon to environment association @@ -24,9 +24,9 @@ organism taxon to environment association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ organism taxon to environment association->organism taxon to entity association - - -uses + + +uses @@ -50,9 +50,9 @@ organism taxon to environment association->id - - -id + + +id @@ -63,9 +63,9 @@ organism taxon to environment association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ organism taxon to environment association->name - - -name + + +name @@ -89,9 +89,9 @@ organism taxon to environment association->description - - -description + + +description @@ -102,9 +102,9 @@ organism taxon to environment association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ organism taxon to environment association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ organism taxon to environment association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ organism taxon to environment association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ organism taxon to environment association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ organism taxon to environment association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ organism taxon to environment association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ organism taxon to environment association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ organism taxon to environment association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ organism taxon to environment association->original subject - - -original subject + + +original subject @@ -232,9 +232,9 @@ organism taxon to environment association->original predicate - - -original predicate + + +original predicate @@ -245,129 +245,272 @@ organism taxon to environment association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +organism taxon to environment association->subject category + + +subject category + + + +object category + +ontology class + + + +organism taxon to environment association->object category + + +object category + + + +subject closure + +string + + + +organism taxon to environment association->subject closure + + +subject closure + + + +object closure + +string + + + +organism taxon to environment association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +organism taxon to environment association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +organism taxon to environment association->object category closure + + +object category closure + + + +subject namespace + +string + + + +organism taxon to environment association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +organism taxon to environment association->object namespace + + +object namespace + + + +subject label closure + +string + + + +organism taxon to environment association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +organism taxon to environment association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +organism taxon to environment association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + organism taxon to environment association->type - - -type + + +type - + category - -category + +category - + organism taxon to environment association->category - - -category + + +category - + subject - -subject + +subject - + organism taxon to environment association->subject - - -subject + + +subject - + object - -object + +object - + organism taxon to environment association->object - - -object + + +object - + predicate - -predicate + +predicate - + organism taxon to environment association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + organism taxon to environment association_subject - -organism taxon + +organism taxon - + object->relation - - + + - + organism taxon to environment association_object - -named thing + +named thing - + organism taxon to environment association_predicate - -predicate type + +predicate type diff --git a/graphviz/organism_taxon_to_organism_taxon_association.gv b/graphviz/organism_taxon_to_organism_taxon_association.gv index 018d50b3b0..a0be43289f 100644 --- a/graphviz/organism_taxon_to_organism_taxon_association.gv +++ b/graphviz/organism_taxon_to_organism_taxon_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3441.4,283"]; + graph [bb="0,0,5165.4,283"]; node [label="\N"]; "organism taxon to organism taxon association" [height=0.5, label="organism taxon to organism taxon association", - pos="1818.4,265", + pos="2801.4,265", width=6.2467]; association [height=0.5, pos="62.394,178", width=1.7332]; "organism taxon to organism taxon association" -> association [label=is_a, - lp="509.39,221.5", - pos="e,106.89,190.69 1595.5,262.48 1332.4,259.68 881.74,251.7 495.39,229 334.12,219.53 292.81,222.21 133.39,196 128,195.11 122.41,194.04 \ -116.84,192.88"]; + lp="499.39,221.5", + pos="e,106.89,190.67 2577.9,262.86 2079.1,259.94 887.68,250.86 485.39,229 328.5,220.47 288.41,221.69 133.39,196 128,195.11 122.41,194.03 \ +116.84,192.86"]; "organism taxon to entity association" [height=0.5, pos="322.39,178", width=5.0009]; "organism taxon to organism taxon association" -> "organism taxon to entity association" [label=uses, - lp="657.89,221.5", - pos="e,401.36,194.21 1599.7,260.79 1311.8,255.98 820.9,245.67 641.39,229 563.24,221.74 475.16,207.47 411.38,196.02"]; + lp="655.89,221.5", + pos="e,399.54,194.27 2576.2,264.36 2101.2,264.46 1009.8,261.05 639.39,229 561.15,222.23 472.96,207.76 409.5,196.11"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "organism taxon to organism taxon association" -> id [color=blue, label=id, - lp="780.39,221.5", - pos="e,587.11,189.94 1599.4,260.83 1341.1,256.35 927.42,246.68 773.39,229 698.23,220.37 679.36,216.02 606.39,196 603.24,195.13 599.99,\ -194.16 596.75,193.14", + lp="775.39,221.5", + pos="e,587.38,190 2578.7,262.48 2088.1,258.79 944.01,248.23 768.39,229 695.35,221 677.2,215.65 606.39,196 603.29,195.14 600.09,194.17 \ +596.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "organism taxon to organism taxon association" -> iri [color=blue, label=iri, - lp="902.39,221.5", - pos="e,692,190.2 1593.2,264.35 1405.7,262.52 1132,254.91 894.39,229 812.67,220.09 792.15,215.93 712.39,196 708.96,195.14 705.43,194.18 \ -701.89,193.17", + lp="892.39,221.5", + pos="e,692.29,190.23 2576.3,264.73 2142.6,265.33 1205.8,262.52 884.39,229 806.98,220.93 787.81,215.26 712.39,196 709.02,195.14 705.54,\ +194.18 702.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "organism taxon to organism taxon association" -> name [color=blue, label=name, - lp="1010.4,221.5", - pos="e,818.2,190.89 1604.5,259.33 1399.4,254.06 1104.5,244.18 990.39,229 934,221.5 870.68,205.55 828.04,193.67", + lp="1004.4,221.5", + pos="e,817.39,191.26 2578.8,262.36 2128.3,258.65 1138.3,248.4 984.39,229 929.75,222.11 868.59,206.19 827.21,194.15", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon association" -> description [color=blue, label=description, - lp="1134.9,221.5", - pos="e,966.99,193.56 1604.6,259.42 1427,254.55 1188.8,245.25 1094.4,229 1053.9,222.04 1009.5,208.3 976.75,196.99", + lp="1132.9,221.5", + pos="e,965.8,193.64 2578,262.85 2148,260.13 1234.9,251.74 1092.4,229 1052,222.56 1007.8,208.65 975.45,197.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "organism taxon to organism taxon association" -> "has attribute" [color=blue, label="has attribute", - lp="1286.4,221.5", - pos="e,1107.2,191.7 1595.3,262.58 1487.1,258.83 1355.8,249.75 1239.4,229 1197,221.43 1150.1,206.69 1117,195.16", + lp="1290.4,221.5", + pos="e,1107,191.74 2578.9,262.24 2179.7,258.61 1371.4,248.9 1243.4,229 1199.3,222.14 1150.5,206.98 1116.6,195.14", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "organism taxon to organism taxon association" -> predicate [color=blue, label=predicate, - lp="1436.4,221.5", - pos="e,1264,193.2 1627.9,255.43 1556.8,250.27 1475.5,242.06 1402.4,229 1358.4,221.14 1309.6,207.36 1273.8,196.25", + lp="1450.4,221.5", + pos="e,1264.6,193.08 2576.5,264.47 2243,264.12 1633.4,259.17 1416.4,229 1367.6,222.22 1313.5,207.75 1274.6,196.12", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "organism taxon to organism taxon association" -> negated [color=blue, label=negated, - lp="1558.4,221.5", - pos="e,1399.6,189.93 1672.8,251.28 1626.7,245.94 1575.7,238.67 1529.4,229 1479.4,218.56 1468.2,210.87 1419.4,196 1416.1,194.99 1412.7,\ -193.95 1409.2,192.9", + lp="1595.4,221.5", + pos="e,1399,190.21 2578.2,262.82 2276.7,260.34 1755.4,252.67 1566.4,229 1511.1,222.07 1449.1,205.34 1408.5,193.13", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "organism taxon to organism taxon association" -> qualifiers [color=blue, label=qualifiers, - lp="1666.9,221.5", - pos="e,1539.3,194.24 1719.7,248.82 1691.5,243.56 1661,236.94 1633.4,229 1604.5,220.71 1573.1,208.5 1548.7,198.21", + lp="1730.9,221.5", + pos="e,1547.9,193 2578.2,262.8 2305.8,260.3 1861.2,252.62 1697.4,229 1649.4,222.07 1596,207.62 1557.8,196.03", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "organism taxon to organism taxon association" -> publications [color=blue, label=publications, - lp="1770.4,221.5", - pos="e,1680.4,195.45 1766.5,247.38 1753.1,242.24 1738.9,236.05 1726.4,229 1713,221.42 1699.3,211.19 1688.1,201.95", + lp="1871.4,221.5", + pos="e,1698.1,192.76 2578.4,262.65 2336.6,259.99 1966.3,252.15 1827.4,229 1786.1,222.11 1740.6,207.8 1707.9,196.25", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon association" -> "has evidence" [color=blue, label="has evidence", - lp="1864.9,221.5", - pos="e,1818.4,196.18 1818.4,246.8 1818.4,235.16 1818.4,219.55 1818.4,206.24", + lp="2022.9,221.5", + pos="e,1855.4,193.77 2581.3,261.2 2377,257.41 2088.1,248.69 1976.4,229 1938,222.24 1896.1,208.65 1865,197.35", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "organism taxon to organism taxon association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2012.9,221.5", - pos="e,1988.1,195.37 1867.6,247.3 1883,241.78 1900,235.41 1915.4,229 1936.7,220.11 1959.9,209.19 1979.1,199.83", + lp="2168.9,221.5", + pos="e,2041.8,195.77 2576.3,264.38 2406.8,262.48 2189.6,254.77 2104.4,229 2085.1,223.17 2065.6,212 2050.3,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "organism taxon to organism taxon association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2235.4,221.5", - pos="e,2209,194.37 1949.8,250.38 1992,244.97 2038.9,237.88 2081.4,229 2121.3,220.66 2165.4,207.94 2199.3,197.41", + lp="2336.4,221.5", + pos="e,2243.3,196.25 2595.8,257.68 2441.2,251.89 2253.8,242.21 2241.4,229 2235.4,222.6 2236,213.84 2239,205.44", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,9 +147,8 @@ digraph { width=3.015]; "organism taxon to organism taxon association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2497.9,221.5", - pos="e,2450.4,194.85 1977.6,252.24 2002.6,250.45 2028.2,248.65 2052.4,247 2177.7,238.45 2211,252.34 2334.4,229 2370.8,222.11 2410.6,209.27 \ -2440.9,198.32", + lp="2544.9,221.5", + pos="e,2456.3,195.1 2605,256.21 2526.1,251.02 2450.7,242.56 2438.4,229 2429.6,219.36 2436.6,209.3 2447.9,200.75", style=solid]; timepoint [color=blue, height=0.5, @@ -159,9 +157,8 @@ digraph { width=1.5346]; "organism taxon to organism taxon association" -> timepoint [color=blue, label=timepoint, - lp="2671.4,221.5", - pos="e,2657.3,195.36 1972.8,251.9 1999.4,250.07 2026.7,248.35 2052.4,247 2114.1,243.76 2550.3,250.07 2608.4,229 2623.9,223.38 2638.6,\ -212.45 2650,202.24", + lp="2694.4,221.5", + pos="e,2661.3,195.8 2702.3,248.74 2682.5,243.65 2665.8,237.14 2659.4,229 2654.1,222.2 2654.6,213.44 2657.3,205.16", style=solid]; "original subject" [color=blue, height=0.5, @@ -170,9 +167,8 @@ digraph { width=1.0652]; "organism taxon to organism taxon association" -> "original subject" [color=blue, label="original subject", - lp="2797.4,221.5", - pos="e,2767.7,194.44 1972.2,251.83 1998.9,250 2026.5,248.3 2052.4,247 2125.4,243.35 2640.8,251.37 2710.4,229 2728.5,223.19 2746.2,211.48 \ -2759.8,200.86", + lp="2791.4,221.5", + pos="e,2758.3,191.31 2754.2,247.32 2746.7,242.57 2739.9,236.56 2735.4,229 2728.1,216.95 2737.5,205.59 2749.8,196.74", style=solid]; "original predicate" [color=blue, height=0.5, @@ -181,85 +177,202 @@ digraph { width=1.5887]; "organism taxon to organism taxon association" -> "original predicate" [color=blue, label="original predicate", - lp="2938.9,221.5", - pos="e,2889.5,196.26 1971.3,251.79 1998.3,249.94 2026.2,248.25 2052.4,247 2097.1,244.88 2817.2,248.58 2857.4,229 2868.2,223.73 2877.2,\ -214.11 2883.9,204.7", + lp="2926.9,221.5", + pos="e,2882.4,195.75 2825.2,246.75 2832.5,241.26 2840.4,235.04 2847.4,229 2856.8,220.85 2866.7,211.38 2875.2,202.9", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3030.4,178", + pos="3012.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "original object" [color=blue, label="original object", - lp="3070.9,221.5", - pos="e,3027.1,196.01 1970.6,251.75 1997.8,249.9 2025.9,248.21 2052.4,247 2078.9,245.79 2984.1,243.33 3006.4,229 3014.7,223.65 3020.2,\ -214.53 3023.8,205.54", + lp="3056.9,221.5", + pos="e,3010.6,196.32 2931.4,250.25 2959.2,245.1 2983.5,238.18 2994.4,229 3001.2,223.24 3005.4,214.7 3008.1,206.3", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3145.4,178", + width=2.1304]; + "organism taxon to organism taxon association" -> "subject category" [color=blue, + label="subject category", + lp="3187.9,221.5", + pos="e,3138.6,196.3 2959.3,252.11 3029,245.77 3098.5,237.53 3112.4,229 3121.5,223.43 3128.6,214.32 3133.8,205.38", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3316.4,178", + width=2.1304]; + "organism taxon to organism taxon association" -> "object category" [color=blue, + label="object category", + lp="3332.9,221.5", + pos="e,3300.2,195.85 2959.9,252.19 3088.1,242.56 3247.9,230.34 3251.4,229 3266.6,223.15 3281.2,212.53 3292.7,202.57", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3449.4,178", + width=1.0652]; + "organism taxon to organism taxon association" -> "subject closure" [color=blue, + label="subject closure", + lp="3469.9,221.5", + pos="e,3436.3,195.25 2958.7,252.09 2984.3,250.29 3010.6,248.53 3035.4,247 3075,244.56 3355.6,243.92 3392.4,229 3406.4,223.32 3419.3,212.69 \ +3429.3,202.68", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3549.4,178", + width=1.0652]; + "organism taxon to organism taxon association" -> "object closure" [color=blue, + label="object closure", + lp="3590.4,221.5", + pos="e,3546.9,196.37 2956.5,251.94 2982.8,250.12 3009.9,248.39 3035.4,247 3062.8,245.51 3505.8,244.58 3528.4,229 3536.2,223.63 3541.1,\ +214.8 3544.2,206.04", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3682.4,178", + width=2.1304]; + "organism taxon to organism taxon association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3748.9,221.5", + pos="e,3674.4,196.19 2955.5,251.86 2982.1,250.03 3009.6,248.32 3035.4,247 3069.2,245.27 3614.3,244.49 3644.4,229 3654.7,223.71 3663,214.21 \ +3669.1,204.91", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3874.4,178", + width=2.1304]; + "organism taxon to organism taxon association" -> "object category closure" [color=blue, + label="object category closure", + lp="3939.9,221.5", + pos="e,3867.7,196.17 2954.3,251.79 2981.3,249.94 3009.2,248.25 3035.4,247 3080.1,244.88 3801.1,250.37 3840.4,229 3850.1,223.74 3857.5,\ +214.38 3863,205.17", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4064.4,178", + width=1.0652]; + "organism taxon to organism taxon association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4112.4,221.5", + pos="e,4057,195.74 2953.6,251.73 2980.8,249.89 3008.9,248.2 3035.4,247 3090.5,244.5 3978.4,254.25 4027.4,229 4037.7,223.68 4045.9,213.99 \ +4051.9,204.56", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4223.4,178", + width=1.0652]; + "organism taxon to organism taxon association" -> "object namespace" [color=blue, + label="object namespace", + lp="4266.4,221.5", + pos="e,4215.4,195.77 2953.3,251.7 2980.6,249.85 3008.8,248.17 3035.4,247 3067.3,245.59 4155.8,243.23 4184.4,229 4195.1,223.66 4203.8,\ +213.84 4210.2,204.31", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4374.4,178", + width=1.0652]; + "organism taxon to organism taxon association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4426.4,221.5", + pos="e,4366.1,195.79 2953,251.68 2980.4,249.83 3008.7,248.15 3035.4,247 3071.4,245.44 4302,244.86 4334.4,229 4345.3,223.69 4354.1,213.87 \ +4360.7,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4545.4,178", + width=1.0652]; + "organism taxon to organism taxon association" -> "object label closure" [color=blue, + label="object label closure", + lp="4593.9,221.5", + pos="e,4536.8,195.81 2952.7,251.67 2980.2,249.81 3008.6,248.13 3035.4,247 3076.2,245.27 4467.6,246.68 4504.4,229 4515.4,223.71 4524.4,\ +213.9 4531.2,204.36", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4707.4,178", + width=2.347]; + "organism taxon to organism taxon association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4755.9,221.5", + pos="e,4698.8,196.29 2952.7,251.64 2980.2,249.78 3008.6,248.12 3035.4,247 3080.7,245.11 4626.6,248.86 4667.4,229 4678.1,223.78 4686.9,\ +214.16 4693.4,204.75", style=solid]; type [height=0.5, - pos="3118.4,178", + pos="4841.4,178", width=0.86659]; "organism taxon to organism taxon association" -> type [color=blue, label=type, - lp="3148.4,221.5", - pos="e,3127.3,195.56 1970.3,251.73 1997.6,249.87 2025.8,248.19 2052.4,247 2082.2,245.67 3105.5,250.27 3126.4,229 3132.5,222.78 3132.7,\ -213.88 3130.6,205.3", + lp="4855.4,221.5", + pos="e,4842.2,196.18 2952.4,251.64 2980,249.78 3008.5,248.11 3035.4,247 3060.3,245.97 4809.9,244.53 4829.4,229 4836.2,223.54 4839.6,214.93 \ +4841.1,206.37", style=solid]; category [height=0.5, - pos="3219.4,178", + pos="4942.4,178", width=1.4263]; "organism taxon to organism taxon association" -> category [color=blue, label=category, - lp="3222.9,221.5", - pos="e,3207.7,195.88 1970.3,251.71 1997.6,249.86 2025.8,248.18 2052.4,247 2114.3,244.25 3111.2,252.91 3168.4,229 3181.2,223.64 3192.6,\ -213.4 3201.3,203.57", + lp="4935.9,221.5", + pos="e,4926.8,195.25 2952.4,251.63 2980,249.77 3008.5,248.11 3035.4,247 3086.5,244.9 4827,245.34 4875.4,229 4891.6,223.53 4907.1,212.51 \ +4919.1,202.2", style=solid]; subject [height=0.5, - pos="3333.4,178", + pos="5056.4,178", width=1.2277]; "organism taxon to organism taxon association" -> subject [color=blue, label=subject, - lp="3316.4,221.5", - pos="e,3316.1,194.76 1970.3,251.69 1997.6,249.84 2025.8,248.16 2052.4,247 2119.3,244.07 3194.4,248.9 3258.4,229 3276.6,223.34 3294.4,\ -211.76 3308.2,201.17", + lp="5032.4,221.5", + pos="e,5037.1,194.33 2952.4,251.62 2980,249.76 3008.5,248.1 3035.4,247 3089.1,244.8 4919.6,243.37 4971.4,229 4992.1,223.25 5013,211.09 \ +5028.9,200.2", style=solid]; object [height=0.5, - pos="3376.4,91", + pos="5099.4,91", width=1.0832]; "organism taxon to organism taxon association" -> object [color=blue, label=object, - lp="3419.4,178", - pos="e,3389.8,108.09 1970,251.68 1997.4,249.83 2025.7,248.15 2052.4,247 2124.2,243.89 3278.9,253.78 3346.4,229 3388.9,213.4 3394.1,186.96 \ -3399.4,142 3400.2,135.38 3401.3,133.39 3399.4,127 3398.4,123.55 3396.9,120.13 3395.1,116.85", + lp="5143.4,178", + pos="e,5112.8,108.09 2952.1,251.64 2979.8,249.77 3008.4,248.1 3035.4,247 3091.7,244.71 5008.8,246.2 5062.4,229 5086.7,221.2 5095,217.1 \ +5109.4,196 5123.3,175.59 5119.5,166.51 5122.4,142 5123.2,135.38 5124.3,133.39 5122.4,127 5121.4,123.55 5119.9,120.13 5118.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2099.4,265", + pos="3082.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2230.4,265", + pos="3213.4,265", width=2.0762]; subject -> object [label=relation, - lp="3371.4,134.5", - pos="e,3358.5,107.23 3334.5,159.55 3335.7,149.57 3338.2,137.07 3343.4,127 3345.6,122.68 3348.5,118.52 3351.7,114.66"]; + lp="5094.4,134.5", + pos="e,5081.5,107.23 5057.5,159.55 5058.7,149.57 5061.2,137.07 5066.4,127 5068.6,122.68 5071.5,118.52 5074.7,114.66"]; relation [height=0.5, - pos="3321.4,18", + pos="5044.4,18", width=1.2999]; - subject -> relation [pos="e,3322.7,36.188 3332.1,159.79 3330,132.48 3326,78.994 3323.5,46.38", + subject -> relation [pos="e,5045.7,36.188 5055.1,159.79 5053,132.48 5049,78.994 5046.5,46.38", style=dotted]; "organism taxon to organism taxon association_subject" [color=blue, height=0.5, label="organism taxon", - pos="2406.4,265", + pos="3389.4,265", width=2.3109]; - object -> relation [pos="e,3334.2,35.54 3363.9,73.889 3357,64.939 3348.2,53.617 3340.4,43.584", + object -> relation [pos="e,5057.2,35.54 5086.9,73.889 5080,64.939 5071.2,53.617 5063.4,43.584", style=dotted]; "organism taxon to organism taxon association_object" [color=blue, height=0.5, label="organism taxon", - pos="2590.4,265", + pos="3573.4,265", width=2.3109]; } diff --git a/graphviz/organism_taxon_to_organism_taxon_association.svg b/graphviz/organism_taxon_to_organism_taxon_association.svg index 10f9cc8f26..6f56555ee1 100644 --- a/graphviz/organism_taxon_to_organism_taxon_association.svg +++ b/graphviz/organism_taxon_to_organism_taxon_association.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to organism taxon association - -organism taxon to organism taxon association + +organism taxon to organism taxon association @@ -24,9 +24,9 @@ organism taxon to organism taxon association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ organism taxon to organism taxon association->organism taxon to entity association - - -uses + + +uses @@ -50,9 +50,9 @@ organism taxon to organism taxon association->id - - -id + + +id @@ -63,9 +63,9 @@ organism taxon to organism taxon association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ organism taxon to organism taxon association->name - - -name + + +name @@ -89,9 +89,9 @@ organism taxon to organism taxon association->description - - -description + + +description @@ -102,9 +102,9 @@ organism taxon to organism taxon association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ organism taxon to organism taxon association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ organism taxon to organism taxon association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ organism taxon to organism taxon association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ organism taxon to organism taxon association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ organism taxon to organism taxon association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ organism taxon to organism taxon association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ organism taxon to organism taxon association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ organism taxon to organism taxon association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ organism taxon to organism taxon association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ organism taxon to organism taxon association->original subject - - -original subject + + +original subject @@ -245,123 +245,266 @@ organism taxon to organism taxon association->original predicate - - -original predicate + + +original predicate original object - -string + +string organism taxon to organism taxon association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +organism taxon to organism taxon association->subject category + + +subject category + + + +object category + +ontology class + + + +organism taxon to organism taxon association->object category + + +object category + + + +subject closure + +string + + + +organism taxon to organism taxon association->subject closure + + +subject closure + + + +object closure + +string + + + +organism taxon to organism taxon association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +organism taxon to organism taxon association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +organism taxon to organism taxon association->object category closure + + +object category closure + + + +subject namespace + +string + + + +organism taxon to organism taxon association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +organism taxon to organism taxon association->object namespace + + +object namespace + + + +subject label closure + +string + + + +organism taxon to organism taxon association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +organism taxon to organism taxon association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +organism taxon to organism taxon association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + organism taxon to organism taxon association->type - - -type + + +type - + category - -category + +category - + organism taxon to organism taxon association->category - - -category + + +category - + subject - -subject + +subject - + organism taxon to organism taxon association->subject - - -subject + + +subject - + object - -object + +object - + organism taxon to organism taxon association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + organism taxon to organism taxon association_subject - -organism taxon + +organism taxon - + object->relation - - + + - + organism taxon to organism taxon association_object - -organism taxon + +organism taxon diff --git a/graphviz/organism_taxon_to_organism_taxon_interaction.gv b/graphviz/organism_taxon_to_organism_taxon_interaction.gv index bc1be18905..99eca71189 100644 --- a/graphviz/organism_taxon_to_organism_taxon_interaction.gv +++ b/graphviz/organism_taxon_to_organism_taxon_interaction.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3691.5,283"]; + graph [bb="0,0,5414.5,283"]; node [label="\N"]; "organism taxon to organism taxon interaction" [height=0.5, label="organism taxon to organism taxon interaction", - pos="1962.9,265", + pos="2855.9,265", width=6.2106]; "organism taxon to organism taxon association" [height=0.5, pos="224.88,178", width=6.2467]; "organism taxon to organism taxon interaction" -> "organism taxon to organism taxon association" [label=is_a, - lp="606.88,221.5", - pos="e,317.59,194.46 1743.8,261.33 1415.1,256.81 809.58,246.44 592.88,229 502.96,221.76 401.4,207.5 327.79,196.06"]; + lp="604.88,221.5", + pos="e,315.55,194.48 2632.6,263.97 2142,263.35 982.54,258.67 590.88,229 500.79,222.18 399.02,207.72 325.71,196.1"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "organism taxon to organism taxon interaction" -> id [color=blue, label=id, - lp="724.88,221.5", - pos="e,534.86,190.01 1741.7,262.31 1438.5,259.22 909.49,250.81 717.88,229 644.01,220.59 625.55,215.79 553.88,196 550.77,195.14 547.57,\ -194.18 544.37,193.17", + lp="719.88,221.5", + pos="e,534.87,189.98 2634,262.74 2124.4,259.52 899.53,249.71 712.88,229 641.15,221.04 623.39,215.43 553.88,196 550.77,195.13 547.58,194.17 \ +544.38,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "organism taxon to organism taxon interaction" -> iri [color=blue, label=iri, - lp="842.88,221.5", - pos="e,639.49,190.16 1744.1,261.25 1466.9,257.06 1004.8,247.54 834.88,229 756.2,220.41 736.6,215.46 659.88,196 656.45,195.13 652.92,194.16 \ -649.38,193.14", + lp="832.88,221.5", + pos="e,639.79,190.19 2634.3,262.44 2144.8,258.66 1000.5,247.92 824.88,229 750.52,220.99 732.27,214.78 659.88,196 656.5,195.12 653.03,\ +194.16 649.54,193.14", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "organism taxon to organism taxon interaction" -> name [color=blue, label=name, - lp="947.88,221.5", - pos="e,764.5,191.18 1742.8,261.82 1486.6,258.36 1079.4,249.72 927.88,229 874.48,221.7 814.71,205.92 774.13,194.03", + lp="939.88,221.5", + pos="e,763.64,191.54 2633.6,262.91 2160.8,260.16 1085.4,251.51 919.88,229 869.1,222.09 812.51,206.58 773.62,194.65", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon interaction" -> description [color=blue, label=description, - lp="1067.4,221.5", - pos="e,911.44,193.95 1740.6,262.89 1508,260.45 1158.6,252.77 1026.9,229 990.38,222.41 950.61,208.97 921.05,197.69", + lp="1060.4,221.5", + pos="e,909.69,194.15 2632.9,263.68 2178.4,262.44 1174.5,256.59 1019.9,229 985.04,222.78 947.3,209.42 919.2,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "organism taxon to organism taxon interaction" -> "has attribute" [color=blue, label="has attribute", - lp="1209.9,221.5", - pos="e,1051.4,192.73 1743.1,261.62 1545.3,258.16 1269.8,249.68 1162.9,229 1127.4,222.14 1088.9,208.11 1060.9,196.66", + lp="1205.9,221.5", + pos="e,1050.5,192.95 2633.1,263.45 2205.6,261.8 1299.7,255.22 1158.9,229 1124.4,222.58 1087.1,208.62 1060,197.07", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "organism taxon to organism taxon interaction" -> negated [color=blue, label=negated, - lp="1358.9,221.5", - pos="e,1172.1,190.33 1742.9,261.61 1620.7,257.84 1466.3,249.03 1329.9,229 1278.3,221.42 1220.5,205.31 1182,193.41", + lp="1360.9,221.5", + pos="e,1171.7,190.46 2632.2,264.63 2271.3,264.67 1576.2,260.46 1331.9,229 1279.3,222.23 1220.6,205.81 1181.7,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "organism taxon to organism taxon interaction" -> qualifiers [color=blue, label=qualifiers, - lp="1489.4,221.5", - pos="e,1320.2,193.28 1751.4,259.15 1660,254.54 1552.2,245.74 1455.9,229 1412.6,221.48 1364.7,207.6 1329.7,196.37", + lp="1499.4,221.5", + pos="e,1320.6,193.2 2632.2,264.78 2297.9,264.84 1684,260.45 1465.9,229 1419.2,222.26 1367.4,207.87 1330.2,196.25", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "organism taxon to organism taxon interaction" -> publications [color=blue, label=publications, - lp="1622.9,221.5", - pos="e,1469.3,193.32 1770.5,255.76 1708.8,250.65 1640.5,242.38 1578.9,229 1544.4,221.52 1506.8,208.14 1478.8,197.11", + lp="1644.9,221.5", + pos="e,1471.6,192.85 2632.3,264.9 2326.2,264.89 1792.7,260.16 1600.9,229 1559.5,222.28 1514,207.95 1481.3,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon interaction" -> "has evidence" [color=blue, label="has evidence", - lp="1762.4,221.5", - pos="e,1623.8,194.37 1826.4,250.69 1790.2,245.52 1751.2,238.48 1715.9,229 1687.5,221.39 1656.9,209.08 1633.2,198.58", + lp="1803.4,221.5", + pos="e,1629.9,193.63 2632.7,263.78 2361.2,262.32 1919.2,255.71 1756.9,229 1716.5,222.35 1672.1,208.52 1639.6,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "organism taxon to organism taxon interaction" -> "knowledge source" [color=blue, label="knowledge source", - lp="1891.4,221.5", - pos="e,1801.2,196.24 1866.4,248.68 1852.4,243.82 1838.7,237.42 1826.9,229 1818.3,222.9 1811.4,213.84 1806.1,205.1", + lp="1958.4,221.5", + pos="e,1819.4,195.61 2637.9,260.95 2376.2,256.52 1963.7,246.83 1893.9,229 1870.8,223.1 1846.8,211.34 1828.1,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "organism taxon to organism taxon interaction" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2058.9,221.5", - pos="e,1984.5,194.65 1959.1,246.59 1957.8,236.37 1958,223.63 1963.9,214 1967,208.82 1971.3,204.35 1976.1,200.52", + lp="2129.9,221.5", + pos="e,2025.8,196.33 2636.2,261.6 2400.5,257.99 2056.8,249.26 2034.9,229 2028.7,223.32 2026.4,214.91 2025.8,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -130,9 +130,8 @@ digraph { width=3.015]; "organism taxon to organism taxon interaction" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2283.4,221.5", - pos="e,2220.2,194.64 2081.9,249.74 2106.2,244.74 2131.3,238.02 2153.9,229 2165.2,224.48 2166.1,219.64 2176.9,214 2187.6,208.42 2199.4,\ -203.13 2210.8,198.44", + lp="2338.4,221.5", + pos="e,2242.1,195.87 2644.9,259 2469.5,253.78 2246.2,244.19 2231.9,229 2224.7,221.43 2228.2,212.05 2235,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -141,8 +140,8 @@ digraph { width=1.5346]; "organism taxon to organism taxon interaction" -> timepoint [color=blue, label=timepoint, - lp="2443.9,221.5", - pos="e,2429.9,195.38 2120.7,252.22 2239.7,243.16 2383.5,231.73 2389.9,229 2397.3,225.82 2410.6,214.01 2422.5,202.67", + lp="2492.9,221.5", + pos="e,2445.3,196.43 2657.2,256.69 2565.8,251.48 2474,242.87 2457.9,229 2451.3,223.36 2448,214.85 2446.4,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.0652]; "organism taxon to organism taxon interaction" -> "original subject" [color=blue, label="original subject", - lp="2560.9,221.5", - pos="e,2536.8,193.27 2121.1,252.24 2146.1,250.44 2171.7,248.64 2195.9,247 2259.6,242.67 2422.3,249.42 2482.9,229 2484.2,228.55 2507.9,\ -212.7 2528.3,198.97", + lp="2590.9,221.5", + pos="e,2542.1,194.82 2675.4,254.33 2608.1,248.85 2545.4,240.69 2534.9,229 2528.2,221.56 2530.8,211.86 2536.3,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.5887]; "organism taxon to organism taxon interaction" -> "original predicate" [color=blue, label="original predicate", - lp="2701.4,221.5", - pos="e,2656.6,195.46 2117.9,252.03 2143.9,250.21 2170.7,248.46 2195.9,247 2242.7,244.29 2574.6,247.05 2617.9,229 2625.2,225.96 2638.1,\ -214.15 2649.4,202.78", + lp="2717.4,221.5", + pos="e,2658.1,195.8 2708.1,251.46 2683.1,246.35 2662.4,239.14 2653.9,229 2648,222.05 2649.3,213.06 2653.2,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -173,102 +170,218 @@ digraph { width=1.0652]; "organism taxon to organism taxon interaction" -> "original object" [color=blue, label="original object", - lp="2831.4,221.5", - pos="e,2784.5,196.31 2116.4,251.9 2142.9,250.06 2170.2,248.34 2195.9,247 2227.6,245.34 2742.2,247.69 2767.9,229 2775.3,223.62 2779.7,\ -214.9 2782.2,206.24", + lp="2841.4,221.5", + pos="e,2783.3,196.07 2809.5,247.23 2801.9,242.47 2794.8,236.48 2789.9,229 2785.5,222.32 2783.7,214 2783.3,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2918.9,178", + width=2.1304]; + "organism taxon to organism taxon interaction" -> "subject category" [color=blue, + label="subject category", + lp="2965.4,221.5", + pos="e,2913.5,196.22 2879.8,246.74 2885.9,241.53 2892.1,235.46 2896.9,229 2902.1,221.97 2906.4,213.49 2909.8,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3089.9,178", + width=2.1304]; + "organism taxon to organism taxon interaction" -> "object category" [color=blue, + label="object category", + lp="3108.4,221.5", + pos="e,3073.8,195.91 2968.7,249.44 2989.3,244.49 3010.2,237.87 3028.9,229 3042.5,222.54 3055.7,212.41 3066.3,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3222.9,178", + width=1.0652]; + "organism taxon to organism taxon interaction" -> "subject closure" [color=blue, + label="subject closure", + lp="3245.4,221.5", + pos="e,3209.8,195.42 3004.3,251.48 3077,244.6 3152.3,236.05 3167.9,229 3181.1,223.04 3193.2,212.72 3202.8,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3322.9,178", + width=1.0652]; + "organism taxon to organism taxon interaction" -> "object closure" [color=blue, + label="object closure", + lp="3365.9,221.5", + pos="e,3321,196.18 3013.1,252.2 3141.6,242.48 3302.4,230.12 3303.9,229 3311.3,223.48 3315.8,214.73 3318.5,206.08", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3455.9,178", + width=2.1304]; + "organism taxon to organism taxon interaction" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3524.4,221.5", + pos="e,3448.5,196.07 3012.8,252.15 3038.3,250.35 3064.3,248.57 3088.9,247 3125.6,244.66 3387.6,246.68 3419.9,229 3429.7,223.61 3437.6,\ +214.23 3443.4,205.04", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3647.9,178", + width=2.1304]; + "organism taxon to organism taxon interaction" -> "object category closure" [color=blue, + label="object category closure", + lp="3715.4,221.5", + pos="e,3641.8,196.1 3009.7,251.93 3036.1,250.1 3063.3,248.37 3088.9,247 3118.1,245.43 3590.4,243.5 3615.9,229 3625.3,223.64 3632.4,214.27 \ +3637.4,205.08", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3837.9,178", + width=1.0652]; + "organism taxon to organism taxon interaction" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3887.9,221.5", + pos="e,3830.9,196.17 3008.4,251.82 3035.2,249.98 3062.9,248.28 3088.9,247 3128.5,245.06 3767.9,247.77 3802.9,229 3812.7,223.74 3820.3,\ +214.38 3825.9,205.17", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3996.9,178", + width=1.0652]; + "organism taxon to organism taxon interaction" -> "object namespace" [color=blue, + label="object namespace", + lp="4040.9,221.5", + pos="e,3989.5,195.72 3007.8,251.77 3034.8,249.92 3062.6,248.23 3088.9,247 3137.2,244.74 3916.9,251.23 3959.9,229 3970.2,223.66 3978.4,\ +213.98 3984.4,204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4147.9,178", + width=1.0652]; + "organism taxon to organism taxon interaction" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4200.9,221.5", + pos="e,4139.9,195.76 3007.2,251.74 3034.3,249.89 3062.4,248.2 3088.9,247 3145.5,244.44 4058.2,254.31 4108.9,229 4119.6,223.65 4128.2,\ +213.83 4134.6,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4318.9,178", + width=1.0652]; + "organism taxon to organism taxon interaction" -> "object label closure" [color=blue, + label="object label closure", + lp="4366.4,221.5", + pos="e,4310.6,195.78 3006.8,251.71 3034.1,249.85 3062.3,248.17 3088.9,247 3121.9,245.55 4249.2,243.55 4278.9,229 4289.7,223.68 4298.6,\ +213.86 4305.2,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4462.9,178", + width=2.347]; + "organism taxon to organism taxon interaction" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4522.4,221.5", + pos="e,4459.9,196 3006.5,251.69 3033.9,249.83 3062.2,248.15 3088.9,247 3126.4,245.38 4408.4,249.46 4439.9,229 4448,223.7 4453.3,214.72 \ +4456.8,205.82", style=solid]; type [height=0.5, - pos="2873.9,178", + pos="4596.9,178", width=0.86659]; "organism taxon to organism taxon interaction" -> type [color=blue, label=type, - lp="2907.9,221.5", - pos="e,2884.9,194.95 2115.7,251.82 2142.4,249.99 2170,248.28 2195.9,247 2215.1,246.05 2873.5,242.75 2886.9,229 2893.3,222.4 2892.5,213.03 \ -2889.2,204.19", + lp="4618.9,221.5", + pos="e,4602,196.18 3006.5,251.66 3033.9,249.8 3062.2,248.13 3088.9,247 3109.8,246.11 4581,243.74 4595.9,229 4601.8,223.09 4603.4,214.51 \ +4603.1,206.12", style=solid]; category [height=0.5, - pos="2974.9,178", + pos="4697.9,178", width=1.4263]; "organism taxon to organism taxon interaction" -> category [color=blue, label=category, - lp="2981.4,221.5", - pos="e,2964.4,195.81 2115.4,251.81 2142.2,249.97 2169.9,248.27 2195.9,247 2236.5,245.02 2890.7,245.6 2927.9,229 2939.9,223.61 2950.4,\ -213.5 2958.3,203.77", + lp="4696.4,221.5", + pos="e,4684.3,195.45 3006.2,251.67 3033.7,249.81 3062.1,248.13 3088.9,247 3131.9,245.18 4598.5,244.06 4638.9,229 4653.5,223.56 4666.9,\ +212.8 4677.3,202.65", style=solid]; "associated environmental context" [height=0.5, - pos="3210.9,178", + pos="4933.9,178", width=4.6399]; "organism taxon to organism taxon interaction" -> "associated environmental context" [color=blue, label="associated environmental context", - lp="3213.4,221.5", - pos="e,3160.9,195.28 2115.1,251.77 2142,249.93 2169.7,248.24 2195.9,247 2378.2,238.36 2836.1,253.94 3016.9,229 3062.6,222.7 3113,209.5 \ -3151,198.25", + lp="4931.4,221.5", + pos="e,4882.6,195.19 3006.2,251.66 3033.7,249.79 3062.1,248.12 3088.9,247 3271.3,239.35 4550.8,252.09 4731.9,229 4780,222.87 4833.1,209.44 \ +4872.8,198.04", style=solid]; subject [height=0.5, - pos="3439.9,178", + pos="5162.9,178", width=1.2277]; "organism taxon to organism taxon interaction" -> subject [color=blue, label=subject, - lp="3404.9,221.5", - pos="e,3417.5,193.58 2114.1,251.7 2141.3,249.85 2169.4,248.17 2195.9,247 2259.3,244.19 3276.2,243.82 3337.9,229 3363,222.96 3389.2,209.97 \ -3408.7,198.75", + lp="5124.9,221.5", + pos="e,5139.7,193.4 3005.9,251.64 3033.5,249.77 3062,248.1 3088.9,247 3198.1,242.52 4949.3,253.18 5055.9,229 5082.4,222.98 5110.2,209.77 \ +5130.8,198.44", style=solid]; object [height=0.5, - pos="3482.9,91", + pos="5205.9,91", width=1.0832]; "organism taxon to organism taxon interaction" -> object [color=blue, label=object, - lp="3532.9,178", - pos="e,3496.3,108.09 2113.8,251.7 2141.1,249.84 2169.3,248.16 2195.9,247 2264.7,243.99 3368.5,247.09 3434.9,229 3463.5,221.21 3475.1,\ -219.7 3492.9,196 3511.6,171.06 3514.8,156.9 3505.9,127 3504.8,123.55 3503.4,120.13 3501.6,116.85", + lp="5255.9,178", + pos="e,5219.3,108.09 3005.9,251.63 3033.5,249.76 3062,248.1 3088.9,247 3146.2,244.66 5099.3,243.33 5154.9,229 5184.7,221.31 5197.1,220.43 \ +5215.9,196 5234.9,171.26 5237.8,156.9 5228.9,127 5227.8,123.55 5226.4,120.13 5224.6,116.85", style=solid]; predicate [height=0.5, - pos="3636.9,178", + pos="5359.9,178", width=1.5165]; "organism taxon to organism taxon interaction" -> predicate [color=blue, label=predicate, - lp="3609.9,221.5", - pos="e,3613,194.32 2113.5,251.69 2140.9,249.83 2169.2,248.15 2195.9,247 2270.2,243.79 3461.5,246.14 3533.9,229 3558.8,223.1 3584.6,210.51 \ -3604.2,199.44", + lp="5332.9,221.5", + pos="e,5336.1,194.36 3005.9,251.62 3033.5,249.75 3062,248.09 3088.9,247 3209.2,242.12 5139.6,256.47 5256.9,229 5281.8,223.17 5307.7,210.57 \ +5327.2,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2242.9,265", + pos="3135.9,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2373.9,265", + pos="3266.9,265", width=2.0762]; "organism taxon to organism taxon interaction_associated environmental context" [color=blue, height=0.5, label=string, - pos="2504.9,265", + pos="3397.9,265", width=1.0652]; subject -> object [label=relation, - lp="3477.9,134.5", - pos="e,3465,107.23 3441,159.55 3442.2,149.57 3444.7,137.07 3449.9,127 3452.1,122.68 3455,118.52 3458.2,114.66"]; + lp="5200.9,134.5", + pos="e,5188,107.23 5164,159.55 5165.2,149.57 5167.7,137.07 5172.9,127 5175.1,122.68 5178,118.52 5181.2,114.66"]; relation [height=0.5, - pos="3427.9,18", + pos="5150.9,18", width=1.2999]; - subject -> relation [pos="e,3429.2,36.188 3438.6,159.79 3436.5,132.48 3432.4,78.994 3430,46.38", + subject -> relation [pos="e,5152.2,36.188 5161.6,159.79 5159.5,132.48 5155.4,78.994 5153,46.38", style=dotted]; "organism taxon to organism taxon interaction_subject" [color=blue, height=0.5, label="organism taxon", - pos="2644.9,265", + pos="3537.9,265", width=2.3109]; - object -> relation [pos="e,3440.7,35.54 3470.4,73.889 3463.5,64.939 3454.7,53.617 3446.9,43.584", + object -> relation [pos="e,5163.7,35.54 5193.4,73.889 5186.5,64.939 5177.7,53.617 5169.9,43.584", style=dotted]; "organism taxon to organism taxon interaction_object" [color=blue, height=0.5, label="organism taxon", - pos="2828.9,265", + pos="3721.9,265", width=2.3109]; "organism taxon to organism taxon interaction_predicate" [color=blue, height=0.5, label="predicate type", - pos="3007.9,265", + pos="3900.9,265", width=2.1665]; } diff --git a/graphviz/organism_taxon_to_organism_taxon_interaction.svg b/graphviz/organism_taxon_to_organism_taxon_interaction.svg index 71b31e0f8e..8d24f0b8d6 100644 --- a/graphviz/organism_taxon_to_organism_taxon_interaction.svg +++ b/graphviz/organism_taxon_to_organism_taxon_interaction.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to organism taxon interaction - -organism taxon to organism taxon interaction + +organism taxon to organism taxon interaction @@ -24,9 +24,9 @@ organism taxon to organism taxon interaction->organism taxon to organism taxon association - - -is_a + + +is_a @@ -37,9 +37,9 @@ organism taxon to organism taxon interaction->id - - -id + + +id @@ -50,9 +50,9 @@ organism taxon to organism taxon interaction->iri - - -iri + + +iri @@ -63,9 +63,9 @@ organism taxon to organism taxon interaction->name - - -name + + +name @@ -76,9 +76,9 @@ organism taxon to organism taxon interaction->description - - -description + + +description @@ -89,9 +89,9 @@ organism taxon to organism taxon interaction->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ organism taxon to organism taxon interaction->negated - - -negated + + +negated @@ -115,9 +115,9 @@ organism taxon to organism taxon interaction->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ organism taxon to organism taxon interaction->publications - - -publications + + +publications @@ -141,9 +141,9 @@ organism taxon to organism taxon interaction->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ organism taxon to organism taxon interaction->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ organism taxon to organism taxon interaction->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ organism taxon to organism taxon interaction->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ organism taxon to organism taxon interaction->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ organism taxon to organism taxon interaction->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ organism taxon to organism taxon interaction->original predicate - - -original predicate + + +original predicate @@ -232,148 +232,291 @@ organism taxon to organism taxon interaction->original object - - -original object + + +original object - + +subject category + +ontology class + + + +organism taxon to organism taxon interaction->subject category + + +subject category + + + +object category + +ontology class + + + +organism taxon to organism taxon interaction->object category + + +object category + + + +subject closure + +string + + + +organism taxon to organism taxon interaction->subject closure + + +subject closure + + + +object closure + +string + + + +organism taxon to organism taxon interaction->object closure + + +object closure + + + +subject category closure + +ontology class + + + +organism taxon to organism taxon interaction->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +organism taxon to organism taxon interaction->object category closure + + +object category closure + + + +subject namespace + +string + + + +organism taxon to organism taxon interaction->subject namespace + + +subject namespace + + + +object namespace + +string + + + +organism taxon to organism taxon interaction->object namespace + + +object namespace + + + +subject label closure + +string + + + +organism taxon to organism taxon interaction->subject label closure + + +subject label closure + + + +object label closure + +string + + + +organism taxon to organism taxon interaction->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +organism taxon to organism taxon interaction->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + organism taxon to organism taxon interaction->type - - -type + + +type - + category - -category + +category - + organism taxon to organism taxon interaction->category - - -category + + +category - + associated environmental context - -associated environmental context + +associated environmental context - + organism taxon to organism taxon interaction->associated environmental context - - -associated environmental context + + +associated environmental context - + subject - -subject + +subject - + organism taxon to organism taxon interaction->subject - - -subject + + +subject - + object - -object + +object - + organism taxon to organism taxon interaction->object - - -object + + +object - + predicate - -predicate + +predicate - + organism taxon to organism taxon interaction->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + organism taxon to organism taxon interaction_associated environmental context - -string + +string - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + organism taxon to organism taxon interaction_subject - -organism taxon + +organism taxon - + object->relation - - + + - + organism taxon to organism taxon interaction_object - -organism taxon + +organism taxon - + organism taxon to organism taxon interaction_predicate - -predicate type + +predicate type diff --git a/graphviz/organism_taxon_to_organism_taxon_specialization.gv b/graphviz/organism_taxon_to_organism_taxon_specialization.gv index 11a00bd249..d2abd3de74 100644 --- a/graphviz/organism_taxon_to_organism_taxon_specialization.gv +++ b/graphviz/organism_taxon_to_organism_taxon_specialization.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3340.5,283"]; + graph [bb="0,0,5072.5,283"]; node [label="\N"]; "organism taxon to organism taxon specialization" [height=0.5, label="organism taxon to organism taxon specialization", - pos="1875.9,265", + pos="2792.9,265", width=6.5716]; "organism taxon to organism taxon association" [height=0.5, pos="224.88,178", width=6.2467]; "organism taxon to organism taxon specialization" -> "organism taxon to organism taxon association" [label=is_a, - lp="606.88,221.5", - pos="e,317.59,194.41 1645.9,260.7 1333.2,255.71 790.47,245.07 592.88,229 502.96,221.69 401.4,207.43 327.79,196.01"]; + lp="604.88,221.5", + pos="e,315.93,194.53 2556.7,263.83 2069.3,262.88 966.64,257.55 590.88,229 500.95,222.17 399.37,207.75 326.08,196.15"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "organism taxon to organism taxon specialization" -> id [color=blue, label=id, - lp="724.88,221.5", - pos="e,534.86,190.01 1643.5,261.6 1358.1,257.85 890.6,248.84 717.88,229 644.02,220.51 625.55,215.79 553.88,196 550.77,195.14 547.57,194.18 \ -544.37,193.17", + lp="720.88,221.5", + pos="e,534.87,189.98 2558.5,262.52 2053.3,258.97 892.66,248.77 713.88,229 641.71,221.02 623.82,215.5 553.88,196 550.77,195.13 547.57,\ +194.17 544.38,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "organism taxon to organism taxon specialization" -> iri [color=blue, label=iri, - lp="843.88,221.5", - pos="e,639.49,190.17 1647.2,260.35 1389.6,255.53 987.12,245.63 835.88,229 756.77,220.3 737.03,215.53 659.88,196 656.45,195.13 652.92,\ -194.16 649.38,193.14", + lp="833.88,221.5", + pos="e,639.79,190.2 2558.9,262.18 2074.6,258.08 993.66,247.02 825.88,229 751.09,220.97 732.7,214.85 659.88,196 656.5,195.13 653.03,194.16 \ +649.54,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "organism taxon to organism taxon specialization" -> name [color=blue, label=name, - lp="947.88,221.5", - pos="e,764.88,191.25 1645.7,260.81 1410.4,256.6 1061.1,247.44 927.88,229 874.65,221.64 815.09,205.95 774.52,194.1", + lp="940.88,221.5", + pos="e,763.84,191.54 2558.2,262.65 2091.6,259.53 1078.7,250.36 920.88,229 869.74,222.08 812.73,206.51 773.63,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon specialization" -> description [color=blue, label=description, - lp="1066.4,221.5", - pos="e,911.2,193.92 1643.3,261.72 1433.1,258.33 1139.8,249.9 1025.9,229 989.62,222.35 950.11,208.91 920.75,197.64", + lp="1061.4,221.5", + pos="e,909.93,194.14 2556.8,263.43 2109.1,261.75 1167.8,255.11 1020.9,229 985.82,222.77 947.82,209.4 919.52,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "organism taxon to organism taxon specialization" -> "has attribute" [color=blue, label="has attribute", - lp="1208.9,221.5", - pos="e,1051.2,192.68 1648.2,260.02 1475,255.64 1251.7,246.72 1161.9,229 1126.7,222.05 1088.4,208.03 1060.6,196.6", + lp="1206.9,221.5", + pos="e,1050.5,192.82 2557.5,263.16 2138.2,261.04 1293.1,253.71 1159.9,229 1124.9,222.52 1087.1,208.39 1059.7,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "organism taxon to organism taxon specialization" -> negated [color=blue, label=negated, - lp="1357.9,221.5", - pos="e,1172.3,190.35 1654.7,258.61 1554.7,253.93 1435.4,245.21 1328.9,229 1277.7,221.22 1220.4,205.22 1182.1,193.4", + lp="1362.9,221.5", + pos="e,1172.1,190.46 2556.4,264.24 2205.3,263.58 1562.9,258.23 1333.9,229 1280.6,222.2 1221,205.66 1181.6,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "organism taxon to organism taxon specialization" -> qualifiers [color=blue, label=qualifiers, - lp="1486.4,221.5", - pos="e,1319.8,193.25 1674.7,255.49 1604.2,250.36 1524.6,242.15 1452.9,229 1410.7,221.27 1364,207.56 1329.6,196.45", + lp="1503.4,221.5", + pos="e,1321.2,193.07 2556.3,264.25 2233.7,263.47 1672.5,257.81 1469.9,229 1422.1,222.2 1369,207.74 1331,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "organism taxon to organism taxon specialization" -> publications [color=blue, label=publications, - lp="1617.9,221.5", - pos="e,1468.7,193.34 1711.7,251.97 1666.6,246.78 1618.1,239.41 1573.9,229 1541,221.24 1505.1,208.09 1478.2,197.22", + lp="1650.9,221.5", + pos="e,1472.6,192.71 2556.5,264.14 2264,263.07 1783.1,256.9 1606.9,229 1563.8,222.18 1516.3,207.69 1482.3,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon specialization" -> "has evidence" [color=blue, label="has evidence", - lp="1749.4,221.5", - pos="e,1621.8,194.68 1779.7,248.51 1754.4,243.37 1727.4,236.89 1702.9,229 1678.3,221.08 1651.9,209.32 1631,199.19", + lp="1805.4,221.5", + pos="e,1630.4,193.61 2557.7,263.03 2300.9,260.74 1906.7,253.22 1758.9,229 1718,222.3 1673.1,208.48 1640.2,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "organism taxon to organism taxon specialization" -> "knowledge source" [color=blue, label="knowledge source", - lp="1872.4,221.5", - pos="e,1795.3,196.34 1830.4,247.23 1821.9,242.42 1813.9,236.41 1807.9,229 1802.6,222.52 1799.3,214.16 1797.2,206.15", + lp="1960.4,221.5", + pos="e,1820,195.59 2565.3,260.02 2320.9,254.96 1958.9,244.92 1895.9,229 1872.4,223.07 1847.9,211.31 1828.9,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "organism taxon to organism taxon specialization" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2054.9,221.5", - pos="e,1995.1,195.19 1906.2,247.07 1916,241.44 1927,235.06 1936.9,229 1947.3,222.63 1949.3,220.1 1959.9,214 1968.3,209.16 1977.4,204.28 \ -1986.2,199.76", + lp="2131.9,221.5", + pos="e,2026.6,196.41 2564.2,260.36 2348.9,255.87 2056.5,246.57 2036.9,229 2030.5,223.34 2027.9,214.82 2027,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "organism taxon to organism taxon specialization" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2279.4,221.5", - pos="e,2218.2,194.43 2054.1,253.07 2086.6,247.78 2119.7,240.09 2149.9,229 2161.3,224.79 2162,219.55 2172.9,214 2184.2,208.22 2196.7,202.83 \ -2208.7,198.09", + lp="2340.4,221.5", + pos="e,2243.1,195.97 2578.7,257.33 2426.1,251.5 2246,241.93 2233.9,229 2226.9,221.54 2230.1,212.18 2236.5,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "organism taxon to organism taxon specialization" -> timepoint [color=blue, label=timepoint, - lp="2442.9,221.5", - pos="e,2429,195.15 2044.3,252.34 2070.3,250.55 2096.8,248.72 2121.9,247 2180.5,242.97 2331.3,250.89 2385.9,229 2393.8,225.82 2408.4,213.68 \ -2421.3,202.16", + lp="2495.9,221.5", + pos="e,2446.4,196.47 2611.5,253.37 2540.8,247.64 2473.6,239.54 2460.9,229 2454.1,223.41 2450.3,214.91 2448.2,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "organism taxon to organism taxon specialization" -> "original subject" [color=blue, label="original subject", - lp="2557.9,221.5", - pos="e,2535.7,192.7 2041.6,252.12 2068.4,250.32 2095.9,248.55 2121.9,247 2201.2,242.26 2403.3,253.55 2478.9,229 2490.5,225.23 2491.6,\ -220.57 2501.9,214 2510,208.79 2518.9,203.21 2527.1,198.07", + lp="2594.9,221.5", + pos="e,2544.1,194.92 2602.9,254.25 2573.4,248.91 2549.3,240.91 2538.9,229 2532.6,221.83 2534.4,212.39 2538.8,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "organism taxon to organism taxon specialization" -> "original predicate" [color=blue, label="original predicate", - lp="2699.4,221.5", - pos="e,2655.3,195.48 2039.3,251.96 2066.8,250.15 2095.2,248.41 2121.9,247 2176.5,244.11 2563,248.99 2613.9,229 2621.6,225.96 2635.6,213.96 \ -2648,202.48", + lp="2722.4,221.5", + pos="e,2660.8,195.76 2700,248.38 2681,243.27 2664.9,236.85 2658.9,229 2653.6,222.16 2654.1,213.39 2656.9,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "organism taxon to organism taxon specialization" -> "original object" [color=blue, label="original object", - lp="2828.4,221.5", - pos="e,2783.1,196.42 2037.9,251.86 2065.9,250.03 2094.7,248.32 2121.9,247 2157.5,245.27 2734.3,248.92 2763.9,229 2771.8,223.69 2776.9,\ -214.87 2780.1,206.11", + lp="2841.4,221.5", + pos="e,2787.3,196.18 2791.5,246.8 2790.5,235.16 2789.2,219.55 2788.1,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2918.9,178", + width=2.1304]; + "organism taxon to organism taxon specialization" -> "subject category" [color=blue, + label="subject category", + lp="2967.4,221.5", + pos="e,2915,196.4 2866.5,247.89 2877.6,243.13 2888.2,236.97 2896.9,229 2903.6,222.84 2908.4,214.24 2911.7,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3089.9,178", + width=2.1304]; + "organism taxon to organism taxon specialization" -> "object category" [color=blue, + label="object category", + lp="3110.4,221.5", + pos="e,3075.1,195.73 2957.6,252.02 2982.8,246.73 3008,239.32 3030.9,229 3044.5,222.83 3057.5,212.54 3067.8,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3222.9,178", + width=1.0652]; + "organism taxon to organism taxon specialization" -> "subject closure" [color=blue, + label="subject closure", + lp="3246.4,221.5", + pos="e,3210.4,195.51 2951.4,251.63 3049.8,243.56 3159.5,233.69 3169.9,229 3182.8,223.16 3194.6,212.86 3203.7,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3322.9,178", + width=1.0652]; + "organism taxon to organism taxon specialization" -> "object closure" [color=blue, + label="object closure", + lp="3366.9,221.5", + pos="e,3321.4,196.19 2961.3,252.33 2987.3,250.54 3013.8,248.72 3038.9,247 3068.4,244.98 3281.2,246.84 3304.9,229 3312.2,223.49 3316.5,\ +214.74 3319.1,206.09", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3455.9,178", + width=2.1304]; + "organism taxon to organism taxon specialization" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3525.4,221.5", + pos="e,3448.8,196.09 2957.9,252.09 2985,250.29 3012.7,248.52 3038.9,247 3081.3,244.54 3383.7,249.5 3420.9,229 3430.6,223.63 3438.3,214.25 \ +3443.9,205.06", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3647.9,178", + width=2.1304]; + "organism taxon to organism taxon specialization" -> "object category closure" [color=blue, + label="object category closure", + lp="3715.4,221.5", + pos="e,3642.2,196.09 2955.3,251.9 2983.1,250.08 3011.8,248.36 3038.9,247 3071,245.39 3589.1,245.06 3616.9,229 3626.1,223.69 3632.9,214.46 \ +3637.8,205.36", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3837.9,178", + width=1.0652]; + "organism taxon to organism taxon specialization" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3887.9,221.5", + pos="e,3830.9,196.18 2954.3,251.8 2982.5,249.96 3011.5,248.27 3038.9,247 3081.3,245.04 3765.5,249.05 3802.9,229 3812.7,223.75 3820.3,\ +214.39 3826,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3996.9,178", + width=1.0652]; + "organism taxon to organism taxon specialization" -> "object namespace" [color=blue, + label="object namespace", + lp="4040.9,221.5", + pos="e,3989.5,195.73 2953.3,251.77 2981.8,249.92 3011.2,248.23 3038.9,247 3090,244.74 3914.4,252.48 3959.9,229 3970.2,223.67 3978.4,213.98 \ +3984.4,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4147.9,178", + width=1.0652]; + "organism taxon to organism taxon specialization" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4200.9,221.5", + pos="e,4139.9,195.76 2952.9,251.72 2981.5,249.88 3011.1,248.19 3038.9,247 3068.6,245.72 4082.3,242.27 4108.9,229 4119.6,223.66 4128.2,\ +213.84 4134.6,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4318.9,178", + width=1.0652]; + "organism taxon to organism taxon specialization" -> "object label closure" [color=blue, + label="object label closure", + lp="4366.4,221.5", + pos="e,4310.6,195.79 2952.6,251.69 2981.3,249.84 3011,248.17 3038.9,247 3073.3,245.56 4247.9,244.15 4278.9,229 4289.7,223.69 4298.6,213.87 \ +4305.2,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4471.9,178", + width=2.347]; + "organism taxon to organism taxon specialization" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4525.4,221.5", + pos="e,4465.9,196.18 2952.3,251.67 2981.1,249.82 3010.9,248.15 3038.9,247 3077.8,245.41 4405.9,247.9 4439.9,229 4449.3,223.74 4456.4,\ +214.39 4461.5,205.18", style=solid]; type [height=0.5, - pos="2873.9,178", + pos="4605.9,178", width=0.86659]; "organism taxon to organism taxon specialization" -> type [color=blue, label=type, - lp="2905.9,221.5", - pos="e,2883.7,195.51 2037.3,251.8 2065.5,249.96 2094.5,248.27 2121.9,247 2143,246.02 2869.1,244.15 2883.9,229 2890.1,222.65 2889.9,213.6 \ -2887.4,204.95", + lp="4623.9,221.5", + pos="e,4608.6,195.98 2951.9,251.67 2980.8,249.81 3010.8,248.13 3038.9,247 3060.5,246.13 4582.6,243.31 4598.9,229 4605.3,223.32 4607.9,\ +214.65 4608.5,206.11", style=solid]; category [height=0.5, - pos="2974.9,178", + pos="4706.9,178", width=1.4263]; "organism taxon to organism taxon specialization" -> category [color=blue, label=category, - lp="2979.4,221.5", - pos="e,2963.8,195.83 2036.9,251.79 2065.2,249.95 2094.4,248.26 2121.9,247 2166.5,244.96 2884.9,246.77 2925.9,229 2938.3,223.64 2949.1,\ -213.53 2957.4,203.8", + lp="4702.4,221.5", + pos="e,4692.1,195.48 2951.9,251.66 2980.8,249.8 3010.8,248.13 3038.9,247 3083.4,245.21 4601.9,243.91 4643.9,229 4659.1,223.59 4673.5,\ +212.83 4684.6,202.68", style=solid]; subject [height=0.5, - pos="3088.9,178", + pos="4820.9,178", width=1.2277]; "organism taxon to organism taxon specialization" -> subject [color=blue, label=subject, - lp="3071.9,221.5", - pos="e,3071.9,194.73 2036.6,251.76 2065,249.92 2094.3,248.23 2121.9,247 2171.5,244.79 2967.6,244 3014.9,229 3032.9,223.29 3050.5,211.71 \ -3064,201.12", + lp="4797.9,221.5", + pos="e,4802.1,194.32 2951.9,251.64 2980.8,249.79 3010.8,248.12 3038.9,247 3133.2,243.24 4647.1,254.76 4737.9,229 4758,223.28 4778.2,211.29 \ +4793.6,200.49", style=solid]; object [height=0.5, - pos="3131.9,91", + pos="4863.9,91", width=1.0832]; "organism taxon to organism taxon specialization" -> object [color=blue, label=object, - lp="3174.9,178", - pos="e,3145.3,108.09 2036.3,251.74 2064.8,249.9 2094.2,248.21 2121.9,247 2176.3,244.62 3050.8,247.88 3101.9,229 3144.3,213.3 3149.5,186.96 \ -3154.9,142 3155.7,135.38 3156.8,133.39 3154.9,127 3153.8,123.55 3152.4,120.13 3150.6,116.85", + lp="4907.9,178", + pos="e,4877.3,108.09 2951.9,251.63 2980.8,249.77 3010.8,248.11 3038.9,247 3088.5,245.04 4780.6,244.45 4827.9,229 4851.8,221.18 4859.8,\ +216.87 4873.9,196 4887.7,175.52 4884,166.51 4886.9,142 4887.7,135.38 4888.8,133.39 4886.9,127 4885.8,123.55 4884.4,120.13 4882.6,\ +116.85", style=solid]; predicate [height=0.5, - pos="3285.9,178", + pos="5017.9,178", width=1.5165]; "organism taxon to organism taxon specialization" -> predicate [color=blue, label=predicate, - lp="3258.9,221.5", - pos="e,3262,194.3 2035.9,251.73 2064.5,249.88 2094.1,248.2 2121.9,247 2239.7,241.93 3068.2,256.39 3182.9,229 3207.7,223.06 3233.6,210.47 \ -3253.2,199.4", + lp="4990.9,221.5", + pos="e,4994.1,194.35 2951.6,251.64 2980.6,249.78 3010.6,248.11 3038.9,247 3143,242.91 4813.4,252.84 4914.9,229 4939.8,223.15 4965.7,210.56 \ +4985.2,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2168.9,265", + pos="3085.9,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2299.9,265", + pos="3216.9,265", width=2.0762]; subject -> object [label=relation, - lp="3126.9,134.5", - pos="e,3114,107.23 3090,159.55 3091.2,149.57 3093.7,137.07 3098.9,127 3101.1,122.68 3104,118.52 3107.2,114.66"]; + lp="4858.9,134.5", + pos="e,4846,107.23 4822,159.55 4823.2,149.57 4825.7,137.07 4830.9,127 4833.1,122.68 4836,118.52 4839.2,114.66"]; relation [height=0.5, - pos="3076.9,18", + pos="4808.9,18", width=1.2999]; - subject -> relation [pos="e,3078.2,36.188 3087.6,159.79 3085.5,132.48 3081.4,78.994 3079,46.38", + subject -> relation [pos="e,4810.2,36.188 4819.6,159.79 4817.5,132.48 4813.4,78.994 4811,46.38", style=dotted]; "organism taxon to organism taxon specialization_subject" [color=blue, height=0.5, label="organism taxon", - pos="2475.9,265", + pos="3392.9,265", width=2.3109]; - object -> relation [pos="e,3089.7,35.54 3119.4,73.889 3112.5,64.939 3103.7,53.617 3095.9,43.584", + object -> relation [pos="e,4821.7,35.54 4851.4,73.889 4844.5,64.939 4835.7,53.617 4827.9,43.584", style=dotted]; "organism taxon to organism taxon specialization_object" [color=blue, height=0.5, label="organism taxon", - pos="2659.9,265", + pos="3576.9,265", width=2.3109]; "organism taxon to organism taxon specialization_predicate" [color=blue, height=0.5, label="predicate type", - pos="2838.9,265", + pos="3755.9,265", width=2.1665]; } diff --git a/graphviz/organism_taxon_to_organism_taxon_specialization.svg b/graphviz/organism_taxon_to_organism_taxon_specialization.svg index ac141eda97..6d1a3e2d57 100644 --- a/graphviz/organism_taxon_to_organism_taxon_specialization.svg +++ b/graphviz/organism_taxon_to_organism_taxon_specialization.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to organism taxon specialization - -organism taxon to organism taxon specialization + +organism taxon to organism taxon specialization @@ -24,9 +24,9 @@ organism taxon to organism taxon specialization->organism taxon to organism taxon association - - -is_a + + +is_a @@ -37,9 +37,9 @@ organism taxon to organism taxon specialization->id - - -id + + +id @@ -50,9 +50,9 @@ organism taxon to organism taxon specialization->iri - - -iri + + +iri @@ -63,9 +63,9 @@ organism taxon to organism taxon specialization->name - - -name + + +name @@ -76,9 +76,9 @@ organism taxon to organism taxon specialization->description - - -description + + +description @@ -89,9 +89,9 @@ organism taxon to organism taxon specialization->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ organism taxon to organism taxon specialization->negated - - -negated + + +negated @@ -115,9 +115,9 @@ organism taxon to organism taxon specialization->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ organism taxon to organism taxon specialization->publications - - -publications + + +publications @@ -141,9 +141,9 @@ organism taxon to organism taxon specialization->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ organism taxon to organism taxon specialization->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ organism taxon to organism taxon specialization->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ organism taxon to organism taxon specialization->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ organism taxon to organism taxon specialization->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ organism taxon to organism taxon specialization->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ organism taxon to organism taxon specialization->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ organism taxon to organism taxon specialization->original object - - -original object + + +original object - + +subject category + +ontology class + + + +organism taxon to organism taxon specialization->subject category + + +subject category + + + +object category + +ontology class + + + +organism taxon to organism taxon specialization->object category + + +object category + + + +subject closure + +string + + + +organism taxon to organism taxon specialization->subject closure + + +subject closure + + + +object closure + +string + + + +organism taxon to organism taxon specialization->object closure + + +object closure + + + +subject category closure + +ontology class + + + +organism taxon to organism taxon specialization->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +organism taxon to organism taxon specialization->object category closure + + +object category closure + + + +subject namespace + +string + + + +organism taxon to organism taxon specialization->subject namespace + + +subject namespace + + + +object namespace + +string + + + +organism taxon to organism taxon specialization->object namespace + + +object namespace + + + +subject label closure + +string + + + +organism taxon to organism taxon specialization->subject label closure + + +subject label closure + + + +object label closure + +string + + + +organism taxon to organism taxon specialization->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +organism taxon to organism taxon specialization->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + organism taxon to organism taxon specialization->type - - -type + + +type - + category - -category + +category - + organism taxon to organism taxon specialization->category - - -category + + +category - + subject - -subject + +subject - + organism taxon to organism taxon specialization->subject - - -subject + + +subject - + object - -object + +object - + organism taxon to organism taxon specialization->object - - -object + + +object - + predicate - -predicate + +predicate - + organism taxon to organism taxon specialization->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + organism taxon to organism taxon specialization_subject - -organism taxon + +organism taxon - + object->relation - - + + - + organism taxon to organism taxon specialization_object - -organism taxon + +organism taxon - + organism taxon to organism taxon specialization_predicate - -predicate type + +predicate type diff --git a/graphviz/organism_to_organism_association.gv b/graphviz/organism_to_organism_association.gv index e37d27307c..eb47fd5725 100644 --- a/graphviz/organism_to_organism_association.gv +++ b/graphviz/organism_to_organism_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "organism to organism association" [height=0.5, label="organism to organism association", - pos="1542.4,265", + pos="2492.4,265", width=4.6399]; association [height=0.5, pos="62.394,178", width=1.7332]; "organism to organism association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1375.7,263.75 1080.7,262.59 478.08,256.76 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2325.6,263.53 1843.4,261.85 469.05,254.85 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "organism to organism association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1377,262.3 1106.5,258.95 581.14,249.93 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,194.16 \ -219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2326.4,263 1863.6,259.95 581.05,249.72 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "organism to organism association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1379,261.26 1133.4,256.66 680.92,246.16 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,194.19 \ -324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2326.4,262.71 1881.8,259.03 685.45,247.51 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ +194.18 325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "organism to organism association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1378.3,261.35 1152.8,257.1 758.81,247.31 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2326.2,262.94 1897.4,259.91 774.95,250.06 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "organism to organism association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1377.8,261.71 1175.3,258.07 843.14,249.19 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2326,263.34 1914.6,261.33 871.38,253.82 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "organism to organism association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1382.1,259.94 1214.6,254.93 963.42,245.06 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2326.5,262.91 1941.1,260.03 1007.5,250.88 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "organism to organism association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1380.2,260.61 1280,256.59 1149.1,247.87 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2325.2,264.7 1998,265.3 1283.8,262.54 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "organism to organism association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1399.4,255.64 1330.5,250.3 1246.8,241.88 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2325.7,263.48 2025.6,261.88 1405.8,255.38 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "organism to organism association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1425.2,252.11 1381.6,246.59 1332,239 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2325.7,263.54 2050.3,262.02 1511.7,255.62 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "organism to organism association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1465.9,248.95 1442.7,243.57 1417.2,236.85 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2325.9,263.48 2076.5,261.83 1617.8,255.2 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "organism to organism association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461.1,195.6 1522,246.8 1506.7,233.96 1485.7,216.27 1468.9,202.19", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2327,262.49 2109.7,259.63 1740.2,251.53 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "organism to organism association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.5,247.13 1578.8,241.7 1587.7,235.42 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2325.3,264.68 2137.4,263.95 1844.9,257.94 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "organism to organism association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1641.8,250.54 1674.8,245.08 1711.4,237.93 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2331,260.26 2154,255.34 1892.9,245.36 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "organism to organism association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.8,195.14 1660.2,252.15 1679.6,250.33 1699.6,248.55 1718.4,247 1836,237.32 1868.1,254.47 1983.4,229 2013.4,222.36 2045.7,209.97 \ -2070.6,199.18", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2330,260.75 2220.2,256.82 2092,248.14 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "organism to organism association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.76 1657.3,251.86 1677.7,250.01 1698.6,248.29 1718.4,247 1777.2,243.17 2194.7,253.3 2248.4,229 2260.4,223.55 2270.9,\ -213.43 2278.8,203.72", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2364.3,253.44 2333.9,248.24 2307.4,240.51 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "organism to organism association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.22 1656.9,251.81 1677.3,249.96 1698.5,248.25 1718.4,247 1787.6,242.66 2277.1,252.28 2342.4,229 2351.2,225.86 2368.2,\ -212.73 2382.5,200.71", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2400,249.85 2390,244.76 2381.1,237.99 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,203 @@ digraph { width=1.5887]; "organism to organism association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.24 1656.4,251.77 1677,249.91 1698.3,248.2 1718.4,247 1760.7,244.46 2443.4,247.82 2481.4,229 2492.1,223.71 2500.8,214.09 \ -2507.4,204.68", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "organism to organism association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.98 1655.9,251.75 1676.7,249.87 1698.2,248.17 1718.4,247 1743.7,245.53 2609.2,242.88 2630.4,229 2638.5,223.68 2643.8,\ -214.69 2647.3,205.79", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2587.1,250.06 2599.4,244.99 2611,238.17 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "organism to organism association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2608,251.94 2665.8,245.1 2726,236.45 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "organism to organism association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.5,195.8 2611.7,252.32 2630.6,250.51 2650.1,248.68 2668.4,247 2714.4,242.78 2832.4,245.91 2875.4,229 2890.3,223.14 2904.5,\ +212.65 2915.8,202.79", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "organism to organism association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.24 2608.8,252.02 2628.7,250.19 2649.1,248.43 2668.4,247 2745.6,241.28 2944.8,258.46 3016.4,229 3030.2,223.31 3042.9,\ +212.68 3052.7,202.67", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "organism to organism association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.34 2607.3,251.91 2627.7,250.05 2648.6,248.32 2668.4,247 2695.2,245.21 3130.4,244.5 3152.4,229 3160.1,223.6 3164.8,214.76 \ +3167.7,206", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "organism to organism association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.18 2606.9,251.83 2627.3,249.97 2648.5,248.26 2668.4,247 2701.7,244.9 3238.8,244.45 3268.4,229 3278.5,223.69 3286.6,\ +214.19 3292.6,204.89", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "organism to organism association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.16 2606.4,251.75 2627,249.89 2648.3,248.19 2668.4,247 2712.5,244.37 3425.7,250.4 3464.4,229 3474,223.72 3481.2,214.36 \ +3486.5,205.15", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "organism to organism association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2605.9,251.72 2626.7,249.85 2648.2,248.16 2668.4,247 2722.9,243.87 3603,254.35 3651.4,229 3661.6,223.66 3669.6,213.97 \ +3675.4,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "organism to organism association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.76 2605.4,251.72 2626.3,249.84 2648,248.14 2668.4,247 2700,245.23 3780.1,243.3 3808.4,229 3818.9,223.7 3827.2,214.03 \ +3833.4,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "organism to organism association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.78 2605.4,251.69 2626.3,249.81 2648,248.12 2668.4,247 2704.2,245.03 3926.3,244.95 3958.4,229 3969.1,223.67 3977.8,213.85 \ +3984.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "organism to organism association" -> "object label closure" [color=blue, + label="object label closure", + lp="4215.9,221.5", + pos="e,4160.1,195.79 2605.4,251.67 2626.3,249.79 2648,248.11 2668.4,247 2708.9,244.8 4091.9,246.79 4128.4,229 4139.3,223.7 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "organism to organism association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.5,196.31 2605,251.69 2626,249.79 2647.9,248.1 2668.4,247 2713.4,244.58 4248.8,248.49 4289.4,229 4300.2,223.79 4309.2,214.18 \ +4315.9,204.77", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "organism to organism association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1655.9,251.71 1676.7,249.84 1698.2,248.15 1718.4,247 1747,245.37 2730.3,249.45 2750.4,229 2756.6,222.69 2756.6,213.66 \ -2754.2,205", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2605,251.67 2626,249.78 2647.9,248.09 2668.4,247 2693.1,245.68 4433,244.44 4452.4,229 4459.2,223.54 4462.6,214.92 \ +4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "organism to organism association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.87 1655.4,251.74 1676.3,249.85 1698,248.15 1718.4,247 1778,243.63 2737.5,252.3 2792.4,229 2804.9,223.68 2816,213.58 2824.5,\ -203.85", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2605,251.67 2626,249.78 2647.9,248.09 2668.4,247 2719.2,244.3 4450.2,245.26 4498.4,229 4514.6,223.53 4530.1,212.51 \ +4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "organism to organism association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.75 1655.4,251.72 1676.3,249.83 1698,248.14 1718.4,247 1783,243.39 2820.7,248.41 2882.4,229 2900.4,223.33 2918,211.75 \ -2931.5,201.16", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2605,251.66 2626,249.77 2647.9,248.09 2668.4,247 2775.2,241.35 4491.3,257.6 4594.4,229 4615.1,223.25 4636,211.09 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "organism to organism association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1655.4,251.7 1676.3,249.82 1698,248.13 1718.4,247 1787.8,243.16 2904.2,252.97 2969.4,229 3011.9,213.39 3017.1,186.96 \ -3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2605,251.65 2626,249.76 2647.9,248.08 2668.4,247 2724.3,244.05 4632,246.12 4685.4,229 4709.7,221.2 4718,217.1 4732.4,\ +196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1765.4,265", + pos="2715.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1896.4,265", + pos="2846.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "organism to organism association_subject" [color=blue, height=0.5, label="individual organism", - pos="2091.4,265", + pos="3041.4,265", width=2.8525]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "organism to organism association_object" [color=blue, height=0.5, label="individual organism", - pos="2314.4,265", + pos="3264.4,265", width=2.8525]; } diff --git a/graphviz/organism_to_organism_association.svg b/graphviz/organism_to_organism_association.svg index 3ca7a592a1..5e3520b9bf 100644 --- a/graphviz/organism_to_organism_association.svg +++ b/graphviz/organism_to_organism_association.svg @@ -4,16 +4,16 @@ - + %3 - + organism to organism association - -organism to organism association + +organism to organism association @@ -24,9 +24,9 @@ organism to organism association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ organism to organism association->id - - -id + + +id @@ -50,9 +50,9 @@ organism to organism association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ organism to organism association->name - - -name + + +name @@ -76,9 +76,9 @@ organism to organism association->description - - -description + + +description @@ -89,9 +89,9 @@ organism to organism association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ organism to organism association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ organism to organism association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ organism to organism association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ organism to organism association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ organism to organism association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ organism to organism association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ organism to organism association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ organism to organism association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ organism to organism association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ organism to organism association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ organism to organism association->original predicate - - -original predicate + + +original predicate original object - -string + +string organism to organism association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +organism to organism association->subject category + + +subject category + + + +object category + +ontology class + + + +organism to organism association->object category + + +object category + + + +subject closure + +string + + + +organism to organism association->subject closure + + +subject closure + + + +object closure + +string + + + +organism to organism association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +organism to organism association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +organism to organism association->object category closure + + +object category closure + + + +subject namespace + +string + + + +organism to organism association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +organism to organism association->object namespace + + +object namespace + + + +subject label closure + +string + + + +organism to organism association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +organism to organism association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +organism to organism association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + organism to organism association->type - - -type + + +type - + category - -category + +category - + organism to organism association->category - - -category + + +category - + subject - -subject + +subject - + organism to organism association->subject - - -subject + + +subject - + object - -object + +object - + organism to organism association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + organism to organism association_subject - -individual organism + +individual organism - + object->relation - - + + - + organism to organism association_object - -individual organism + +individual organism diff --git a/graphviz/organismal_entity_as_a_model_of_disease_association.gv b/graphviz/organismal_entity_as_a_model_of_disease_association.gv index 1fad83eb87..335ce5f944 100644 --- a/graphviz/organismal_entity_as_a_model_of_disease_association.gv +++ b/graphviz/organismal_entity_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4256.4,283"]; + graph [bb="0,0,5972.4,283"]; node [label="\N"]; "organismal entity as a model of disease association" [height=0.5, label="organismal entity as a model of disease association", - pos="2243.4,265", + pos="3219.4,265", width=6.9147]; association [height=0.5, pos="62.394,178", width=1.7332]; "organismal entity as a model of disease association" -> association [label=is_a, - lp="632.39,221.5", - pos="e,106.73,190.67 1997.2,262.26 1678.8,259.19 1107,250.91 618.39,229 403,219.34 347.58,228.21 134.39,196 128.62,195.13 122.62,194.03 \ -116.67,192.81"]; + lp="626.39,221.5", + pos="e,107.11,190.75 2972.8,262.44 2414.4,258.62 1066.8,247.72 612.39,229 399.62,220.23 344.94,227.91 134.39,196 128.7,195.14 122.79,\ +194.05 116.92,192.86"]; "model to disease association mixin" [height=0.5, pos="315.39,178", width=4.7843]; "organismal entity as a model of disease association" -> "model to disease association mixin" [label=uses, - lp="852.89,221.5", - pos="e,425.49,191.85 1995.7,263.14 1714.5,260.92 1242,253.48 836.39,229 698.66,220.69 541.01,204.64 435.54,192.97"]; + lp="843.89,221.5", + pos="e,423.07,192.13 2971.9,262.98 2447.4,260.38 1238.4,252.04 827.39,229 691.91,221.41 536.89,205.21 433.25,193.3"]; "entity to disease association mixin" [height=0.5, pos="676.39,178", width=4.7482]; "organismal entity as a model of disease association" -> "entity to disease association mixin" [label=uses, lp="998.89,221.5", - pos="e,751.79,194.22 2000.2,261.13 1690.5,256.81 1172.8,247.12 982.39,229 907.39,221.86 822.94,207.59 761.78,196.11"]; + pos="e,750.52,194.23 2970.4,264.7 2470.7,265.34 1361.4,262.75 982.39,229 906.84,222.27 821.76,207.8 760.52,196.15"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "organismal entity as a model of disease association" -> id [color=blue, label=id, - lp="1115.4,221.5", - pos="e,932.39,189.97 1999,261.51 1718.1,257.75 1274.3,248.84 1108.4,229 1037.6,220.53 1020,215.28 951.39,196 948.29,195.13 945.09,194.16 \ -941.89,193.14", + lp="1116.4,221.5", + pos="e,932.38,189.97 2972.8,262.53 2455.5,259.08 1289.8,249.15 1109.4,229 1038.1,221.04 1020.5,215.35 951.39,196 948.29,195.13 945.09,\ +194.16 941.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,8 @@ digraph { width=1.2277]; "organismal entity as a model of disease association" -> iri [color=blue, label=iri, - lp="1218.4,221.5", - pos="e,1037.3,190.11 2001.2,260.78 1744.9,256.49 1357.5,247.21 1210.4,229 1141.4,220.45 1124.6,213.98 1057.4,196 1054,195.1 1050.6,194.11 \ -1047.1,193.09", + lp="1213.4,221.5", + pos="e,1037.7,190.02 2972.7,262.5 2473.4,259.07 1376.1,249.31 1205.4,229 1149.9,222.4 1087.8,205.4 1047.5,193.05", style=solid]; name [color=blue, height=0.5, @@ -53,8 +52,8 @@ digraph { width=1.5707]; "organismal entity as a model of disease association" -> name [color=blue, label=name, - lp="1310.4,221.5", - pos="e,1158.3,192.29 1997.8,262.05 1761.5,258.89 1421.2,250.62 1290.4,229 1247.9,221.97 1201,207.28 1167.7,195.64", + lp="1309.4,221.5", + pos="e,1157.7,192.37 2971.3,263.29 2487.5,261.36 1450.9,254.29 1289.4,229 1247.1,222.37 1200.5,207.67 1167.5,195.91", style=solid]; description [color=blue, height=0.5, @@ -63,8 +62,8 @@ digraph { width=2.0943]; "organismal entity as a model of disease association" -> description [color=blue, label=description, - lp="1414.9,221.5", - pos="e,1298.4,195.09 2006,259.52 1769.8,254.24 1434,244.21 1374.4,229 1350.8,222.97 1326.2,210.96 1307.2,200.23", + lp="1412.9,221.5", + pos="e,1297.8,195.26 2973.3,262.24 2488.2,258.36 1448.6,247.91 1372.4,229 1349.1,223.22 1325,211.22 1306.5,200.42", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +73,7 @@ digraph { "organismal entity as a model of disease association" -> "has attribute" [color=blue, label="has attribute", lp="1532.4,221.5", - pos="e,1434.3,195.29 2004,259.96 1800.3,255.37 1533.4,246.17 1485.4,229 1469.4,223.28 1454,212.34 1442.1,202.15", + pos="e,1434,195.2 2971.7,262.99 2509.1,260.54 1554.3,252.64 1485.4,229 1469.2,223.45 1453.7,212.42 1441.7,202.13", style=solid]; predicate [color=blue, height=0.5, @@ -84,18 +83,18 @@ digraph { "organismal entity as a model of disease association" -> predicate [color=blue, label=predicate, lp="1632.4,221.5", - pos="e,1572.5,196.02 1999.3,261.4 1831.6,257.81 1633.2,249.26 1598.4,229 1589.1,223.61 1582.1,214.35 1577.1,205.26", + pos="e,1572.4,196.14 2970.3,264.74 2530.5,265.19 1657,261.9 1598.4,229 1589,223.7 1581.9,214.34 1576.8,205.14", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="3642.4,91", + pos="5358.4,91", width=1.9318]; "organismal entity as a model of disease association" -> object [color=blue, label=object, lp="1711.4,178", - pos="e,3572.7,91.747 2054.5,253.27 1903.5,242.68 1713.2,223.98 1689.4,196 1679,183.82 1678.3,171.51 1689.4,160 1755.5,91.603 3204,90.853 \ -3562.6,91.721", + pos="e,5288.9,91.949 2976.2,261.08 2655.5,256.61 2108.5,246.68 1908.4,229 1806.7,220.02 1617.9,232.83 1689.4,160 1754.5,93.7 4748.8,91.768 \ +5278.7,91.946", style=solid]; negated [color=blue, height=0.5, @@ -104,9 +103,8 @@ digraph { width=1.2999]; "organismal entity as a model of disease association" -> negated [color=blue, label=negated, - lp="1983.4,221.5", - pos="e,1824.6,189.93 2092.6,250.67 2047.9,245.39 1998.9,238.3 1954.4,229 1904.4,218.56 1893.2,210.87 1844.4,196 1841.1,194.99 1837.7,\ -193.95 1834.2,192.9", + lp="2019.4,221.5", + pos="e,1824.1,190.32 2972.4,262.62 2669.4,259.94 2173.4,252.06 1990.4,229 1935.6,222.1 1874.3,205.5 1833.9,193.31", style=solid]; qualifiers [color=blue, height=0.5, @@ -115,8 +113,8 @@ digraph { width=2.1304]; "organismal entity as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2091.9,221.5", - pos="e,1964.3,194.24 2142.7,248.46 2115.2,243.26 2085.4,236.76 2058.4,229 2029.5,220.71 1998.1,208.5 1973.7,198.21", + lp="2153.9,221.5", + pos="e,1972.8,193.12 2972.6,262.6 2700,259.9 2278.5,252.03 2120.4,229 2073,222.1 2020.4,207.72 1982.6,196.15", style=solid]; publications [color=blue, height=0.5, @@ -125,8 +123,8 @@ digraph { width=1.7332]; "organismal entity as a model of disease association" -> publications [color=blue, label=publications, - lp="2195.4,221.5", - pos="e,2105.4,195.45 2191.5,247.38 2178.1,242.24 2163.9,236.05 2151.4,229 2138,221.42 2124.3,211.19 2113.1,201.95", + lp="2293.4,221.5", + pos="e,2122.8,192.88 2972.8,262.47 2732,259.64 2383.1,251.64 2249.4,229 2208.9,222.14 2164.4,207.9 2132.3,196.37", style=solid]; "has evidence" [color=blue, height=0.5, @@ -135,8 +133,8 @@ digraph { width=2.0943]; "organismal entity as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2289.9,221.5", - pos="e,2243.4,196.18 2243.4,246.8 2243.4,235.16 2243.4,219.55 2243.4,206.24", + lp="2442.9,221.5", + pos="e,2279.5,193.89 2976.7,260.98 2774.8,257.12 2503.6,248.42 2396.4,229 2359.3,222.28 2318.8,208.76 2288.8,197.47", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -145,8 +143,8 @@ digraph { width=3.015]; "organismal entity as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2437.9,221.5", - pos="e,2413.1,195.37 2292.6,247.3 2308,241.78 2325,235.41 2340.4,229 2361.7,220.11 2384.9,209.19 2404.1,199.83", + lp="2586.9,221.5", + pos="e,2464.8,195.77 2988.1,258.34 2802.5,252.81 2566.1,243.14 2522.4,229 2504.6,223.23 2486.9,212.21 2472.9,201.98", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -155,8 +153,8 @@ digraph { width=3.015]; "organismal entity as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2660.4,221.5", - pos="e,2634,194.37 2378.9,249.86 2420,244.52 2465.3,237.6 2506.4,229 2546.3,220.66 2590.4,207.94 2624.3,197.41", + lp="2754.4,221.5", + pos="e,2664.7,195.98 2996.1,257.01 2845.3,251.16 2671.3,241.71 2659.4,229 2653,222.18 2654.7,213.11 2659.2,204.57", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -165,8 +163,8 @@ digraph { width=3.015]; "organismal entity as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2922.9,221.5", - pos="e,2875.4,194.8 2419.7,252.29 2567.5,242.43 2755.1,229.82 2759.4,229 2795.8,222.03 2835.6,209.19 2865.9,198.27", + lp="2963.9,221.5", + pos="e,2877,194.99 3010.1,255.25 2936.5,249.99 2869,241.75 2857.4,229 2848.2,218.83 2855.8,208.72 2868.3,200.28", style=solid]; timepoint [color=blue, height=0.5, @@ -175,9 +173,8 @@ digraph { width=1.5346]; "organismal entity as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3091.4,221.5", - pos="e,3079.3,195.24 2414.7,251.94 2443.7,250.12 2473.4,248.4 2501.4,247 2560.5,244.06 2977.8,249.2 3033.4,229 3041.8,225.94 3057.6,213.6 \ -3071.5,201.95", + lp="3112.4,221.5", + pos="e,3082.8,195.52 3119.2,248.45 3099.9,243.41 3083.7,236.99 3077.4,229 3071.7,221.76 3073.4,212.7 3077.5,204.28", style=solid]; "original subject" [color=blue, height=0.5, @@ -187,8 +184,7 @@ digraph { "organismal entity as a model of disease association" -> "original subject" [color=blue, label="original subject", lp="3209.4,221.5", - pos="e,3187.3,192.7 2414,251.86 2443.2,250.04 2473.1,248.33 2501.4,247 2571.2,243.7 3063.7,249.88 3130.4,229 3142,225.36 3143.1,220.57 \ -3153.4,214 3161.6,208.79 3170.4,203.21 3178.7,198.07", + pos="e,3180.7,190.29 3172.2,247.32 3164.7,242.57 3157.9,236.56 3153.4,229 3145.4,215.65 3157,203.87 3171.8,195.09", style=solid]; "original predicate" [color=blue, height=0.5, @@ -197,9 +193,8 @@ digraph { width=1.5887]; "organismal entity as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3350.9,221.5", - pos="e,3306.9,195.51 2413,251.8 2442.5,249.97 2472.8,248.28 2501.4,247 2543.8,245.1 3225.8,244.25 3265.4,229 3273.2,226.01 3287.2,214.01 \ -3299.5,202.52", + lp="3346.9,221.5", + pos="e,3305.1,195.28 3242.5,246.83 3249.9,241.23 3258.1,234.94 3265.4,229 3276.1,220.35 3287.6,210.53 3297.5,201.9", style=solid]; "original object" [color=blue, height=0.5, @@ -208,93 +203,211 @@ digraph { width=1.0652]; "organismal entity as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3479.9,221.5", - pos="e,3434.7,195.96 2412.3,251.75 2442,249.92 2472.6,248.23 2501.4,247 2526.8,245.91 3394.3,243.09 3415.4,229 3423.4,223.65 3428.5,214.66 \ -3431.8,205.76", + lp="3478.9,221.5", + pos="e,3433.9,195.93 3350.5,249.67 3378.5,244.53 3403.1,237.76 3414.4,229 3422,223.14 3427.1,214.2 3430.6,205.49", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3570.4,178", + width=2.1304]; + "organismal entity as a model of disease association" -> "subject category" [color=blue, + label="subject category", + lp="3610.9,221.5", + pos="e,3562.6,196.33 3420.9,254.39 3469.5,249.21 3513.4,241.25 3534.4,229 3544,223.42 3551.7,214.17 3557.5,205.14", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3741.4,178", + width=2.1304]; + "organismal entity as a model of disease association" -> "object category" [color=blue, + label="object category", + lp="3756.9,221.5", + pos="e,3724.8,195.61 3390.7,251.92 3516.8,242.85 3667.5,231.57 3674.4,229 3690.1,223.12 3705.2,212.38 3717.1,202.36", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3874.4,178", + width=1.0652]; + "organismal entity as a model of disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3892.9,221.5", + pos="e,3858.6,194.67 3394.2,252.18 3422.1,250.38 3450.5,248.6 3477.4,247 3552.7,242.52 3746.4,257.14 3816.4,229 3824.3,225.84 3838.7,\ +213.42 3851.2,201.75", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3970.4,178", + width=1.0652]; + "organismal entity as a model of disease association" -> "object closure" [color=blue, + label="object closure", + lp="4011.4,221.5", + pos="e,3967.9,196.36 3391.8,251.98 3420.4,250.17 3449.7,248.44 3477.4,247 3503.6,245.64 3927.8,243.94 3949.4,229 3957.2,223.63 3962.1,\ +214.79 3965.2,206.03", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4103.4,178", + width=2.1304]; + "organismal entity as a model of disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4169.9,221.5", + pos="e,4095.4,196.19 3390.4,251.88 3419.4,250.07 3449.3,248.36 3477.4,247 3510,245.43 4036.3,243.97 4065.4,229 4075.7,223.7 4084,214.21 \ +4090.1,204.91", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4292.4,178", + width=2.1304]; + "organismal entity as a model of disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4359.9,221.5", + pos="e,4286.7,196.12 3389,251.79 3418.5,249.96 3448.8,248.27 3477.4,247 3520.9,245.07 4223.6,250.62 4261.4,229 4270.6,223.73 4277.4,214.5 \ +4282.3,205.4", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4482.4,178", + width=1.0652]; + "organismal entity as a model of disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4532.4,221.5", + pos="e,4475.4,196.2 3388,251.74 3417.7,249.91 3448.5,248.22 3477.4,247 3531.2,244.73 4399.8,254.33 4447.4,229 4457.2,223.77 4464.9,214.42 \ +4470.5,205.21", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4641.4,178", + width=1.0652]; + "organismal entity as a model of disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4685.4,221.5", + pos="e,4634,195.74 3387.6,251.7 3417.5,249.86 3448.4,248.19 3477.4,247 3508.7,245.72 4576.5,243.31 4604.4,229 4614.7,223.69 4622.9,214.01 \ +4628.9,204.57", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4792.4,178", + width=1.0652]; + "organismal entity as a model of disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4845.4,221.5", + pos="e,4784.4,195.78 3387.3,251.68 3417.3,249.83 3448.2,248.17 3477.4,247 3512.8,245.58 4721.7,244.78 4753.4,229 4764.1,223.67 4772.8,\ +213.85 4779.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4963.4,178", + width=1.0652]; + "organismal entity as a model of disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="5010.9,221.5", + pos="e,4955.1,195.79 3386.9,251.66 3417,249.81 3448.1,248.15 3477.4,247 3517.5,245.43 4887.3,246.63 4923.4,229 4934.3,223.7 4943.1,213.88 \ +4949.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5107.4,178", + width=2.347]; + "organismal entity as a model of disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5166.9,221.5", + pos="e,5104.4,196.01 3386.6,251.65 3416.8,249.8 3448,248.13 3477.4,247 3522,245.28 5046.9,253.29 5084.4,229 5092.5,223.71 5097.9,214.73 \ +5101.3,205.83", style=solid]; type [height=0.5, - pos="3525.4,178", + pos="5241.4,178", width=0.86659]; "organismal entity as a model of disease association" -> type [color=blue, label=type, - lp="3557.4,221.5", - pos="e,3535.3,195.52 2412,251.72 2441.7,249.88 2472.5,248.2 2501.4,247 2530.1,245.81 3515.3,249.49 3535.4,229 3541.6,222.67 3541.4,213.63 \ -3538.9,204.97", + lp="5263.4,221.5", + pos="e,5246.5,196.18 3386.6,251.62 3416.8,249.78 3448,248.12 3477.4,247 3501.9,246.07 5223,246.23 5240.4,229 5246.4,223.09 5248,214.52 \ +5247.6,206.13", style=solid]; category [height=0.5, - pos="3626.4,178", + pos="5342.4,178", width=1.4263]; "organismal entity as a model of disease association" -> category [color=blue, label=category, - lp="3630.9,221.5", - pos="e,3615.3,195.86 2411.6,251.72 2441.5,249.88 2472.4,248.2 2501.4,247 2561.1,244.53 3522.5,252.62 3577.4,229 3589.8,223.67 3600.6,\ -213.57 3609,203.84", + lp="5340.9,221.5", + pos="e,5328.8,195.46 3386.6,251.62 3416.8,249.77 3448,248.11 3477.4,247 3527.5,245.1 5236.4,246.51 5283.4,229 5298,223.57 5311.4,212.81 \ +5321.8,202.66", style=solid]; subject [height=0.5, - pos="3740.4,178", + pos="5456.4,178", width=1.2277]; "organismal entity as a model of disease association" -> subject [color=blue, label=subject, - lp="3723.4,221.5", - pos="e,3723.4,194.75 2411.6,251.69 2441.5,249.85 2472.4,248.18 2501.4,247 2566.1,244.37 3604.6,248.43 3666.4,229 3684.4,223.34 3702,211.75 \ -3715.5,201.16", + lp="5435.4,221.5", + pos="e,5438.1,194.56 3386.2,251.63 3416.5,249.77 3447.9,248.11 3477.4,247 3530.1,245.02 5325.8,243.78 5376.4,229 5395.8,223.32 5415.2,\ +211.45 5430,200.71", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3887.4,178", + pos="5603.4,178", width=2.3651]; "organismal entity as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3874.4,221.5", - pos="e,3855,194.69 2411.3,251.68 2441.3,249.84 2472.2,248.17 2501.4,247 2640.4,241.42 3616.7,254.69 3753.4,229 3785.5,222.98 3819.9,209.97 \ -3845.8,198.73", + lp="5588.4,221.5", + pos="e,5570.3,194.62 3386.2,251.62 3416.5,249.76 3447.9,248.1 3477.4,247 3587.8,242.87 5356.7,248.59 5465.4,229 5498.5,223.04 5534.1,\ +209.96 5560.8,198.68", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4066.4,178", + pos="5782.4,178", width=2.1123]; "organismal entity as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4055.4,221.5", - pos="e,4037.3,194.83 2410.9,251.66 2441,249.81 2472.1,248.15 2501.4,247 2581.6,243.86 3867.8,245.23 3946.4,229 3975,223.1 4005.2,210.42 \ -4028.3,199.31", + lp="5770.4,221.5", + pos="e,5752.8,194.86 3386.2,251.6 3416.5,249.75 3447.9,248.09 3477.4,247 3598.6,242.51 5541.5,252.93 5660.4,229 5689.4,223.17 5720.2,\ +210.48 5743.6,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4203.4,178", + pos="5919.4,178", width=1.011]; "organismal entity as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4204.9,221.5", - pos="e,4185.3,193.83 2410.6,251.65 2440.8,249.8 2472,248.13 2501.4,247 2591.3,243.54 4033.9,253.57 4120.4,229 4141,223.15 4161.7,210.73 \ -4177.2,199.74", + lp="5920.9,221.5", + pos="e,5901,193.86 3385.9,251.6 3416.3,249.74 3447.8,248.09 3477.4,247 3542.9,244.6 5772.3,246.61 5835.4,229 5856.2,223.19 5877.1,210.77 \ +5892.9,199.77", style=solid]; relation [height=0.5, - pos="3691.4,18", + pos="5407.4,18", width=1.2999]; - object -> relation [pos="e,3679.9,35.705 3654,73.174 3660,64.509 3667.4,53.768 3674,44.141", + object -> relation [pos="e,5395.9,35.705 5370,73.174 5376,64.509 5383.4,53.768 5390,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="2548.4,265", + pos="3524.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2679.4,265", + pos="3655.4,265", width=2.0762]; subject -> object [label=relation, - lp="3698.4,134.5", - pos="e,3648.8,108.97 3707.9,165.59 3695.1,159.94 3681,152.13 3670.4,142 3663.4,135.31 3657.7,126.48 3653.3,118.1"]; - subject -> relation [pos="e,3702.6,35.828 3739,159.99 3736.9,139.02 3732,102.55 3721.4,73 3717.9,63.258 3712.8,53.189 3707.8,44.423", + lp="5414.4,134.5", + pos="e,5364.8,108.97 5423.9,165.59 5411.1,159.94 5397,152.13 5386.4,142 5379.4,135.31 5373.7,126.48 5369.3,118.1"]; + subject -> relation [pos="e,5418.6,35.828 5455,159.99 5452.9,139.02 5448,102.55 5437.4,73 5433.9,63.258 5428.8,53.189 5423.8,44.423", style=dotted]; "organismal entity as a model of disease association_subject" [color=blue, height=0.5, label="organismal entity", - pos="2865.4,265", + pos="3841.4,265", width=2.5817]; } diff --git a/graphviz/organismal_entity_as_a_model_of_disease_association.svg b/graphviz/organismal_entity_as_a_model_of_disease_association.svg index 60cf6c2534..3db6b721b4 100644 --- a/graphviz/organismal_entity_as_a_model_of_disease_association.svg +++ b/graphviz/organismal_entity_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + organismal entity as a model of disease association - -organismal entity as a model of disease association + +organismal entity as a model of disease association @@ -24,9 +24,9 @@ organismal entity as a model of disease association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ organismal entity as a model of disease association->model to disease association mixin - - -uses + + +uses @@ -50,8 +50,8 @@ organismal entity as a model of disease association->entity to disease association mixin - - + + uses @@ -63,9 +63,9 @@ organismal entity as a model of disease association->id - - -id + + +id @@ -76,9 +76,9 @@ organismal entity as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ organismal entity as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ organismal entity as a model of disease association->description - - -description + + +description @@ -115,8 +115,8 @@ organismal entity as a model of disease association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ organismal entity as a model of disease association->predicate - - + + predicate object - -named thing + +named thing organismal entity as a model of disease association->object - - + + object @@ -154,9 +154,9 @@ organismal entity as a model of disease association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ organismal entity as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ organismal entity as a model of disease association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ organismal entity as a model of disease association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ organismal entity as a model of disease association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ organismal entity as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ organismal entity as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ organismal entity as a model of disease association->timepoint - - -timepoint + + +timepoint @@ -258,8 +258,8 @@ organismal entity as a model of disease association->original subject - - + + original subject @@ -271,9 +271,9 @@ organismal entity as a model of disease association->original predicate - - -original predicate + + +original predicate @@ -284,130 +284,273 @@ organismal entity as a model of disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +organismal entity as a model of disease association->subject category + + +subject category + + + +object category + +ontology class + + + +organismal entity as a model of disease association->object category + + +object category + + + +subject closure + +string + + + +organismal entity as a model of disease association->subject closure + + +subject closure + + + +object closure + +string + + + +organismal entity as a model of disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +organismal entity as a model of disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +organismal entity as a model of disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +organismal entity as a model of disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +organismal entity as a model of disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +organismal entity as a model of disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +organismal entity as a model of disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +organismal entity as a model of disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + organismal entity as a model of disease association->type - - -type + + +type - + category - -category + +category - + organismal entity as a model of disease association->category - - -category + + +category - + subject - -subject + +subject - + organismal entity as a model of disease association->subject - - -subject + + +subject - + frequency qualifier - -frequency value + +frequency value - + organismal entity as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + organismal entity as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + organismal entity as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + relation - -relation + +relation - + object->relation - - + + - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + subject->relation - - + + - + organismal entity as a model of disease association_subject - -organismal entity + +organismal entity diff --git a/graphviz/pairwise_gene_to_gene_interaction.gv b/graphviz/pairwise_gene_to_gene_interaction.gv index c5032352c4..c7e85e0ee0 100644 --- a/graphviz/pairwise_gene_to_gene_interaction.gv +++ b/graphviz/pairwise_gene_to_gene_interaction.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3142,283"]; + graph [bb="0,0,4874,283"]; node [label="\N"]; "pairwise gene to gene interaction" [height=0.5, label="pairwise gene to gene interaction", - pos="1677.4,265", + pos="2594.4,265", width=4.6399]; "gene to gene association" [height=0.5, pos="125.44,178", width=3.4844]; "pairwise gene to gene interaction" -> "gene to gene association" [label=is_a, - lp="408.44,221.5", - pos="e,188.35,193.58 1511.6,262.71 1215.3,259.85 605.92,251.4 394.44,229 327.4,221.9 252.02,207.31 198.15,195.71"]; + lp="406.44,221.5", + pos="e,187.32,193.67 2428.2,262.98 1950,259.82 592.45,249.17 392.44,229 325.77,222.28 250.85,207.61 197.38,195.89"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "pairwise gene to gene interaction" -> id [color=blue, label=id, - lp="526.44,221.5", - pos="e,336.42,190.01 1512,262.43 1239.1,259.26 706.46,250.49 519.44,229 445.57,220.51 427.11,215.79 355.44,196 352.33,195.14 349.13,194.18 \ -345.93,193.17", + lp="522.44,221.5", + pos="e,336.43,189.98 2428.1,262.98 1968.5,259.93 702.8,249.72 515.44,229 443.27,221.02 425.38,215.5 355.44,196 352.33,195.13 349.13,194.17 \ +345.93,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "pairwise gene to gene interaction" -> iri [color=blue, label=iri, - lp="645.44,221.5", - pos="e,441.05,190.17 1513.3,261.51 1264.2,257.22 802.03,247.09 637.44,229 558.33,220.3 538.59,215.53 461.44,196 458.01,195.13 454.48,\ -194.16 450.94,193.14", + lp="635.44,221.5", + pos="e,441.35,190.2 2428.4,262.75 1986.5,259.17 803.6,247.92 627.44,229 552.65,220.97 534.26,214.85 461.44,196 458.06,195.13 454.58,194.16 \ +451.1,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "pairwise gene to gene interaction" -> name [color=blue, label=name, - lp="749.44,221.5", - pos="e,566.44,191.25 1512.8,261.91 1282.5,258.3 875.76,249.24 729.44,229 676.21,221.64 616.65,205.95 576.08,194.1", + lp="742.44,221.5", + pos="e,565.4,191.54 2428.3,263.09 2001.4,260.45 888.48,251.48 722.44,229 671.3,222.08 614.29,206.51 575.18,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "pairwise gene to gene interaction" -> description [color=blue, label=description, - lp="867.94,221.5", - pos="e,712.76,193.92 1511.5,262.68 1302.1,260.05 954.01,252.22 827.44,229 791.17,222.35 751.67,208.91 722.31,197.64", + lp="862.94,221.5", + pos="e,711.49,194.14 2427.7,263.67 2016.8,262.42 977.42,256.55 822.44,229 787.38,222.77 749.38,209.4 721.08,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "pairwise gene to gene interaction" -> "has attribute" [color=blue, label="has attribute", - lp="1010.4,221.5", - pos="e,852.79,192.68 1513.4,261.49 1335.9,257.78 1064.7,248.99 963.44,229 928.22,222.05 889.94,208.03 862.16,196.6", + lp="1008.4,221.5", + pos="e,852.02,192.82 2427.7,263.48 2040.5,261.83 1102.5,255.15 961.44,229 926.48,222.52 888.61,208.39 861.24,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "pairwise gene to gene interaction" -> negated [color=blue, label=negated, - lp="1159.4,221.5", - pos="e,973.83,190.35 1514.5,260.99 1405.3,257.16 1258.6,248.5 1130.4,229 1079.3,221.22 1022,205.22 983.65,193.4", + lp="1164.4,221.5", + pos="e,973.64,190.46 2427.5,264.31 2099.2,264.21 1380.6,260.29 1135.4,229 1082.1,222.2 1022.5,205.66 983.19,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "pairwise gene to gene interaction" -> qualifiers [color=blue, label=qualifiers, - lp="1287.9,221.5", - pos="e,1121.4,193.25 1521.8,258.47 1441.4,253.76 1342.1,245.07 1254.4,229 1212.2,221.27 1165.6,207.56 1131.2,196.45", + lp="1304.9,221.5", + pos="e,1122.7,193.07 2427.5,264.35 2123.2,264.2 1489.5,260.01 1271.4,229 1223.6,222.2 1170.6,207.74 1132.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "pairwise gene to gene interaction" -> publications [color=blue, label=publications, - lp="1419.4,221.5", - pos="e,1270.2,193.34 1539.5,254.8 1487.6,249.57 1428.4,241.47 1375.4,229 1342.5,221.24 1306.7,208.09 1279.7,197.22", + lp="1452.4,221.5", + pos="e,1274.2,192.71 2427.5,264.31 2148.6,263.95 1599.5,259.24 1408.4,229 1365.3,222.18 1317.8,207.69 1283.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "pairwise gene to gene interaction" -> "has evidence" [color=blue, label="has evidence", - lp="1550.9,221.5", - pos="e,1423.3,194.68 1587.6,249.77 1560.5,244.44 1531,237.54 1504.4,229 1479.8,221.08 1453.4,209.32 1432.5,199.19", + lp="1606.9,221.5", + pos="e,1431.9,193.61 2427.9,263.56 2179.1,262.01 1722.2,255.51 1560.4,229 1519.6,222.3 1474.7,208.48 1441.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "pairwise gene to gene interaction" -> "knowledge source" [color=blue, label="knowledge source", - lp="1673.9,221.5", - pos="e,1596.8,196.34 1632.6,247.63 1624,242.75 1615.6,236.61 1609.4,229 1604.2,222.52 1600.9,214.16 1598.8,206.15", + lp="1761.9,221.5", + pos="e,1621.5,195.59 2430.6,261.28 2191.1,256.74 1766.2,246.38 1697.4,229 1673.9,223.07 1649.5,211.31 1630.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "pairwise gene to gene interaction" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1856.4,221.5", - pos="e,1796.7,195.19 1707.4,247.25 1717.4,241.57 1728.4,235.12 1738.4,229 1748.8,222.63 1750.9,220.1 1761.4,214 1769.8,209.16 1778.9,\ -204.28 1787.7,199.76", + lp="1933.4,221.5", + pos="e,1828.2,196.41 2430,261.61 2214.2,257.71 1860.1,248.4 1838.4,229 1832.1,223.34 1829.4,214.82 1828.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "pairwise gene to gene interaction" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2080.9,221.5", - pos="e,2019.7,194.43 1791.5,251.85 1859.8,244.15 1936.1,234.63 1951.4,229 1962.9,224.79 1963.6,219.55 1974.4,214 1985.7,208.22 1998.2,\ -202.83 2010.2,198.09", + lp="2141.9,221.5", + pos="e,2044.7,195.97 2435.8,259.34 2275.4,253.84 2049.1,243.55 2035.4,229 2028.4,221.54 2031.6,212.18 2038.1,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "pairwise gene to gene interaction" -> timepoint [color=blue, label=timepoint, - lp="2244.4,221.5", - pos="e,2230.5,195.19 1793.8,252.06 1813.7,250.22 1834.2,248.45 1853.4,247 1927.6,241.43 2118.3,256.18 2187.4,229 2195.4,225.88 2210,213.74 \ -2222.8,202.2", + lp="2297.4,221.5", + pos="e,2248,196.47 2448.9,256.08 2366.6,250.3 2277.3,241.32 2262.4,229 2255.7,223.41 2251.9,214.91 2249.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "pairwise gene to gene interaction" -> "original subject" [color=blue, label="original subject", - lp="2359.4,221.5", - pos="e,2337.3,192.7 1792.9,251.95 1813,250.1 1833.8,248.36 1853.4,247 1948.2,240.43 2190,257.97 2280.4,229 2292.1,225.28 2293.2,220.57 \ -2303.4,214 2311.6,208.79 2320.5,203.21 2328.7,198.07", + lp="2396.4,221.5", + pos="e,2345.7,194.92 2436.9,258.91 2393.5,254.01 2354.4,245.06 2340.4,229 2334.2,221.83 2336,212.39 2340.4,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "pairwise gene to gene interaction" -> "original predicate" [color=blue, label="original predicate", - lp="2500.9,221.5", - pos="e,2456.9,195.49 1791.9,251.87 1812.4,250 1833.5,248.28 1853.4,247 1915.8,242.99 2357.2,251.69 2415.4,229 2423.2,225.98 2437.2,213.98 \ -2449.5,202.49", + lp="2523.9,221.5", + pos="e,2462.4,195.76 2506.5,249.65 2485.4,244.35 2467,237.52 2460.4,229 2455.2,222.16 2455.7,213.39 2458.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "pairwise gene to gene interaction" -> "original object" [color=blue, label="original object", - lp="2629.9,221.5", - pos="e,2584.7,196.43 1791.4,251.8 1812,249.93 1833.4,248.22 1853.4,247 1892.9,244.6 2532.6,251.04 2565.4,229 2573.3,223.7 2578.4,214.89 \ -2581.7,206.12", + lp="2642.9,221.5", + pos="e,2588.9,196.18 2593,246.8 2592.1,235.16 2590.8,219.55 2589.7,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2720.4,178", + width=2.1304]; + "pairwise gene to gene interaction" -> "subject category" [color=blue, + label="subject category", + lp="2768.9,221.5", + pos="e,2716.6,196.4 2666.2,248.69 2677.9,243.82 2689.2,237.42 2698.4,229 2705.2,222.84 2710,214.24 2713.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2891.4,178", + width=2.1304]; + "pairwise gene to gene interaction" -> "object category" [color=blue, + label="object category", + lp="2911.9,221.5", + pos="e,2876.6,195.73 2714.8,252.46 2762.5,246.61 2811,238.68 2832.4,229 2846.1,222.83 2859,212.54 2869.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3024.4,178", + width=1.0652]; + "pairwise gene to gene interaction" -> "subject closure" [color=blue, + label="subject closure", + lp="3047.9,221.5", + pos="e,3012,195.53 2713.7,252.37 2732.7,250.55 2752.1,248.71 2770.4,247 2815.1,242.84 2930.5,247.4 2971.4,229 2984.4,223.18 2996.1,212.88 \ +3005.3,203.13", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3124.4,178", + width=1.0652]; + "pairwise gene to gene interaction" -> "object closure" [color=blue, + label="object closure", + lp="3168.4,221.5", + pos="e,3123,196.23 2710.8,252.05 2730.7,250.21 2751.2,248.45 2770.4,247 2807.7,244.2 3076.4,251.31 3106.4,229 3113.8,223.54 3118.1,214.8 \ +3120.7,206.15", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3257.4,178", + width=2.1304]; + "pairwise gene to gene interaction" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3326.9,221.5", + pos="e,3250.4,196.11 2709.9,251.91 2730,250.07 2750.8,248.34 2770.4,247 2820.6,243.58 3178.3,253.09 3222.4,229 3232.2,223.67 3239.8,214.3 \ +3245.5,205.1", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3449.4,178", + width=2.1304]; + "pairwise gene to gene interaction" -> "object category closure" [color=blue, + label="object category closure", + lp="3516.9,221.5", + pos="e,3443.7,196.1 2708.4,251.84 2729,249.97 2750.4,248.25 2770.4,247 2806.4,244.77 3387.2,246.95 3418.4,229 3427.6,223.71 3434.5,214.48 \ +3439.4,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3639.4,178", + width=1.0652]; + "pairwise gene to gene interaction" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3689.4,221.5", + pos="e,3632.5,196.19 2708,251.78 2728.7,249.9 2750.2,248.19 2770.4,247 2816.7,244.27 3563.6,250.84 3604.4,229 3614.3,223.76 3621.9,214.4 \ +3627.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3798.4,178", + width=1.0652]; + "pairwise gene to gene interaction" -> "object namespace" [color=blue, + label="object namespace", + lp="3842.4,221.5", + pos="e,3791.1,195.74 2707.9,251.72 2728.7,249.85 2750.2,248.16 2770.4,247 2825.4,243.85 3712.5,254.23 3761.4,229 3771.8,223.68 3780,213.99 \ +3786,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3949.4,178", + width=1.0652]; + "pairwise gene to gene interaction" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4002.4,221.5", + pos="e,3941.5,195.77 2707.5,251.72 2728.4,249.84 2750.1,248.14 2770.4,247 2802.1,245.23 3882.1,243.12 3910.4,229 3921.2,223.66 3929.8,\ +213.84 3936.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4120.4,178", + width=1.0652]; + "pairwise gene to gene interaction" -> "object label closure" [color=blue, + label="object label closure", + lp="4167.9,221.5", + pos="e,4112.1,195.79 2707.5,251.69 2728.4,249.81 2750.1,248.12 2770.4,247 2806.8,245 4047.7,244.99 4080.4,229 4091.3,223.69 4100.1,213.87 \ +4106.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4273.4,178", + width=2.347]; + "pairwise gene to gene interaction" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4326.9,221.5", + pos="e,4267.5,196.18 2707.5,251.67 2728.4,249.79 2750.1,248.11 2770.4,247 2811.2,244.78 4205.7,248.84 4241.4,229 4250.9,223.75 4258,214.39 \ +4263,205.18", style=solid]; type [height=0.5, - pos="2675.4,178", + pos="4407.4,178", width=0.86659]; "pairwise gene to gene interaction" -> type [color=blue, label=type, - lp="2707.4,221.5", - pos="e,2685.3,195.51 1791,251.78 1811.7,249.9 1833.2,248.19 1853.4,247 1876.5,245.64 2669.3,245.52 2685.4,229 2691.6,222.66 2691.5,213.61 \ -2688.9,204.96", + lp="4425.4,221.5", + pos="e,4410.1,195.98 2707,251.69 2728.1,249.79 2749.9,248.1 2770.4,247 2793,245.79 4383.4,243.95 4400.4,229 4406.9,223.32 4409.4,214.65 \ +4410.1,206.12", style=solid]; category [height=0.5, - pos="2776.4,178", + pos="4508.4,178", width=1.4263]; "pairwise gene to gene interaction" -> category [color=blue, label=category, - lp="2780.9,221.5", - pos="e,2765.4,195.84 1791,251.76 1811.7,249.89 1833.2,248.18 1853.4,247 1901.9,244.16 2682.9,248.27 2727.4,229 2739.8,223.65 2750.7,213.55 \ -2759,203.82", + lp="4503.9,221.5", + pos="e,4493.7,195.48 2707,251.68 2728.1,249.79 2749.9,248.1 2770.4,247 2816.9,244.51 4401.6,244.55 4445.4,229 4460.7,223.59 4475,212.84 \ +4486.2,202.68", style=solid]; subject [height=0.5, - pos="2890.4,178", + pos="4622.4,178", width=1.2277]; "pairwise gene to gene interaction" -> subject [color=blue, label=subject, - lp="2873.4,221.5", - pos="e,2873.4,194.73 1791,251.73 1811.7,249.86 1833.2,248.16 1853.4,247 1906.9,243.93 2765.4,245.14 2816.4,229 2834.4,223.31 2852,211.72 \ -2865.6,201.14", + lp="4599.4,221.5", + pos="e,4603.7,194.32 2707,251.67 2728.1,249.78 2749.9,248.09 2770.4,247 2868.6,241.77 4444.9,255.8 4539.4,229 4559.6,223.29 4579.8,211.3 \ +4595.2,200.49", style=solid]; object [height=0.5, - pos="2933.4,91", + pos="4665.4,91", width=1.0832]; "pairwise gene to gene interaction" -> object [color=blue, label=object, - lp="2976.4,178", - pos="e,2946.8,108.09 1790.5,251.75 1811.4,249.86 1833.1,248.16 1853.4,247 1911.7,243.69 2848.7,249.2 2903.4,229 2945.9,213.33 2951.1,\ -186.96 2956.4,142 2957.2,135.38 2958.3,133.39 2956.4,127 2955.4,123.55 2953.9,120.13 2952.2,116.85", + lp="4709.4,178", + pos="e,4678.8,108.09 2707,251.67 2728.1,249.77 2749.9,248.09 2770.4,247 2822,244.26 4580.4,245.05 4629.4,229 4653.4,221.18 4661.4,216.87 \ +4675.4,196 4689.2,175.52 4685.5,166.51 4688.4,142 4689.2,135.38 4690.3,133.39 4688.4,127 4687.4,123.55 4685.9,120.13 4684.2,116.85", style=solid]; predicate [height=0.5, - pos="3087.4,178", + pos="4819.4,178", width=1.5165]; "pairwise gene to gene interaction" -> predicate [color=blue, label=predicate, - lp="3060.4,221.5", - pos="e,3063.6,194.3 1790.5,251.73 1811.4,249.84 1833.1,248.14 1853.4,247 1978.9,239.95 2862.2,258.13 2984.4,229 3009.3,223.07 3035.2,\ -210.48 3054.8,199.41", + lp="4792.4,221.5", + pos="e,4795.6,194.36 2707,251.66 2728.1,249.77 2749.9,248.08 2770.4,247 2878.4,241.3 4611.2,253.71 4716.4,229 4741.3,223.16 4767.2,210.56 \ +4786.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1900.4,265", + pos="2817.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2031.4,265", + pos="2948.4,265", width=2.0762]; subject -> object [label=relation, - lp="2928.4,134.5", - pos="e,2915.5,107.23 2891.5,159.55 2892.7,149.57 2895.2,137.07 2900.4,127 2902.7,122.68 2905.6,118.52 2908.8,114.66"]; + lp="4660.4,134.5", + pos="e,4647.5,107.23 4623.5,159.55 4624.7,149.57 4627.2,137.07 4632.4,127 4634.7,122.68 4637.6,118.52 4640.8,114.66"]; relation [height=0.5, - pos="2878.4,18", + pos="4610.4,18", width=1.2999]; - subject -> relation [pos="e,2879.7,36.188 2889.1,159.79 2887.1,132.48 2883,78.994 2880.5,46.38", + subject -> relation [pos="e,4611.7,36.188 4621.1,159.79 4619.1,132.48 4615,78.994 4612.5,46.38", style=dotted]; "gene to gene association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="2234.4,265", + pos="3151.4,265", width=3.0692]; - object -> relation [pos="e,2891.3,35.54 2921,73.889 2914,64.939 2905.3,53.617 2897.5,43.584", + object -> relation [pos="e,4623.3,35.54 4653,73.889 4646,64.939 4637.3,53.617 4629.5,43.584", style=dotted]; "gene to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="2473.4,265", + pos="3390.4,265", width=3.0692]; "pairwise gene to gene interaction_predicate" [color=blue, height=0.5, label="predicate type", - pos="2679.4,265", + pos="3596.4,265", width=2.1665]; } diff --git a/graphviz/pairwise_gene_to_gene_interaction.svg b/graphviz/pairwise_gene_to_gene_interaction.svg index 1e99ac8e9c..3ea0e5a47a 100644 --- a/graphviz/pairwise_gene_to_gene_interaction.svg +++ b/graphviz/pairwise_gene_to_gene_interaction.svg @@ -4,16 +4,16 @@ - + %3 - + pairwise gene to gene interaction - -pairwise gene to gene interaction + +pairwise gene to gene interaction @@ -24,9 +24,9 @@ pairwise gene to gene interaction->gene to gene association - - -is_a + + +is_a @@ -37,9 +37,9 @@ pairwise gene to gene interaction->id - - -id + + +id @@ -50,9 +50,9 @@ pairwise gene to gene interaction->iri - - -iri + + +iri @@ -63,9 +63,9 @@ pairwise gene to gene interaction->name - - -name + + +name @@ -76,9 +76,9 @@ pairwise gene to gene interaction->description - - -description + + +description @@ -89,9 +89,9 @@ pairwise gene to gene interaction->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ pairwise gene to gene interaction->negated - - -negated + + +negated @@ -115,9 +115,9 @@ pairwise gene to gene interaction->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ pairwise gene to gene interaction->publications - - -publications + + +publications @@ -141,9 +141,9 @@ pairwise gene to gene interaction->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ pairwise gene to gene interaction->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ pairwise gene to gene interaction->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ pairwise gene to gene interaction->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ pairwise gene to gene interaction->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ pairwise gene to gene interaction->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ pairwise gene to gene interaction->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ pairwise gene to gene interaction->original object - - -original object + + +original object - + +subject category + +ontology class + + + +pairwise gene to gene interaction->subject category + + +subject category + + + +object category + +ontology class + + + +pairwise gene to gene interaction->object category + + +object category + + + +subject closure + +string + + + +pairwise gene to gene interaction->subject closure + + +subject closure + + + +object closure + +string + + + +pairwise gene to gene interaction->object closure + + +object closure + + + +subject category closure + +ontology class + + + +pairwise gene to gene interaction->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +pairwise gene to gene interaction->object category closure + + +object category closure + + + +subject namespace + +string + + + +pairwise gene to gene interaction->subject namespace + + +subject namespace + + + +object namespace + +string + + + +pairwise gene to gene interaction->object namespace + + +object namespace + + + +subject label closure + +string + + + +pairwise gene to gene interaction->subject label closure + + +subject label closure + + + +object label closure + +string + + + +pairwise gene to gene interaction->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +pairwise gene to gene interaction->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + pairwise gene to gene interaction->type - - -type + + +type - + category - -category + +category - + pairwise gene to gene interaction->category - - -category + + +category - + subject - -subject + +subject - + pairwise gene to gene interaction->subject - - -subject + + +subject - + object - -object + +object - + pairwise gene to gene interaction->object - - -object + + +object - + predicate - -predicate + +predicate - + pairwise gene to gene interaction->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene to gene association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene to gene association_object - -gene or gene product + +gene or gene product - + pairwise gene to gene interaction_predicate - -predicate type + +predicate type diff --git a/graphviz/pairwise_molecular_interaction.gv b/graphviz/pairwise_molecular_interaction.gv index 3af6261936..9cec1236bf 100644 --- a/graphviz/pairwise_molecular_interaction.gv +++ b/graphviz/pairwise_molecular_interaction.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3397,283"]; + graph [bb="0,0,5127,283"]; node [label="\N"]; "pairwise molecular interaction" [height=0.5, label="pairwise molecular interaction", - pos="1983,265", + pos="2800,265", width=4.2427]; "pairwise gene to gene interaction" [height=0.5, pos="167.04,178", width=4.6399]; "pairwise molecular interaction" -> "pairwise gene to gene interaction" [label=is_a, lp="503.04,221.5", - pos="e,244.77,193.99 1831.1,262.96 1504.9,260.32 745.93,251.86 489.04,229 409.34,221.91 319.42,207.39 254.9,195.82"]; + pos="e,243.77,193.99 2647.3,264.46 2201.9,265.35 909.98,264.7 489.04,229 408.91,222.21 318.49,207.54 253.91,195.84"]; iri [color=blue, height=0.5, label="iri type", @@ -19,8 +19,8 @@ digraph { "pairwise molecular interaction" -> iri [color=blue, label=iri, lp="623.04,221.5", - pos="e,428.94,190.2 1830.7,263.38 1525,261.59 846.36,254.76 615.04,229 540.28,220.67 521.86,214.85 449.04,196 445.66,195.13 442.18,194.16 \ -438.7,193.15", + pos="e,428.94,190.2 2647.9,263.15 2185.4,260.35 815.22,250.32 615.04,229 540.24,221.03 521.86,214.85 449.04,196 445.66,195.13 442.18,\ +194.16 438.7,193.15", style=solid]; name [color=blue, height=0.5, @@ -30,7 +30,7 @@ digraph { "pairwise molecular interaction" -> name [color=blue, label=name, lp="730.04,221.5", - pos="e,553.01,191.44 1830.3,264.06 1540.8,263.46 921.88,258.63 710.04,229 658.93,221.85 601.91,206.32 562.8,194.45", + pos="e,552.63,191.45 2647.8,263.5 2198.9,261.75 899.93,254.52 710.04,229 658.73,222.11 601.52,206.45 562.41,194.48", style=solid]; description [color=blue, height=0.5, @@ -40,7 +40,7 @@ digraph { "pairwise molecular interaction" -> description [color=blue, label=description, lp="850.54,221.5", - pos="e,699.4,194.16 1832.2,262.04 1538,257.84 907.8,246.89 810.04,229 775.12,222.61 737.26,209.32 708.98,198.05", + pos="e,699.09,194.17 2647.3,264.07 2212.6,263.89 988.63,260.54 810.04,229 774.97,222.81 736.97,209.44 708.67,198.08", style=solid]; "has attribute" [color=blue, height=0.5, @@ -49,8 +49,8 @@ digraph { width=1.4443]; "pairwise molecular interaction" -> "has attribute" [color=blue, label="has attribute", - lp="997.04,221.5", - pos="e,840.14,192.82 1830.3,264.59 1585,264.57 1114,260.26 950.04,229 915,222.32 876.99,208.28 849.43,196.77", + lp="996.04,221.5", + pos="e,839.62,192.85 2647.3,263.96 2234,263.46 1113.5,259.29 949.04,229 914.06,222.56 876.2,208.43 848.84,196.83", style=solid]; negated [color=blue, height=0.5, @@ -59,8 +59,8 @@ digraph { width=1.2999]; "pairwise molecular interaction" -> negated [color=blue, label=negated, - lp="1154,221.5", - pos="e,961.62,190.28 1833.6,261.25 1625.1,256.85 1257.5,246.82 1125,229 1071.3,221.76 1011,205.31 971.27,193.25", + lp="1151,221.5", + pos="e,961.05,190.49 2648.3,262.66 2263.7,259.01 1270.7,247.85 1122,229 1069.1,222.28 1009.9,205.79 970.8,193.57", style=solid]; qualifiers [color=blue, height=0.5, @@ -69,8 +69,8 @@ digraph { width=2.1304]; "pairwise molecular interaction" -> qualifiers [color=blue, label=qualifiers, - lp="1287.5,221.5", - pos="e,1110.3,193.16 1834.6,260.63 1654.6,255.89 1361.8,245.88 1254,229 1207.9,221.78 1156.8,207.58 1119.9,196.15", + lp="1290.5,221.5", + pos="e,1109.9,193.12 2648.7,262.6 2286.9,258.95 1392,248.1 1257,229 1209.7,222.3 1157.2,207.82 1119.6,196.17", style=solid]; publications [color=blue, height=0.5, @@ -79,8 +79,8 @@ digraph { width=1.7332]; "pairwise molecular interaction" -> publications [color=blue, label=publications, - lp="1426,221.5", - pos="e,1260.2,193.01 1836.9,259.68 1687.6,254.51 1466,244.56 1382,229 1343.3,221.83 1300.9,207.92 1269.9,196.59", + lp="1438,221.5", + pos="e,1261.3,192.76 2648.8,262.48 2310.9,258.76 1515.1,248.07 1394,229 1351.4,222.28 1304.4,207.78 1270.9,196.12", style=solid]; "has evidence" [color=blue, height=0.5, @@ -89,8 +89,8 @@ digraph { width=2.0943]; "pairwise molecular interaction" -> "has evidence" [color=blue, label="has evidence", - lp="1573.5,221.5", - pos="e,1416.3,193.91 1832.3,261.99 1742.8,258.44 1627.5,249.72 1527,229 1492.3,221.84 1454.4,208.71 1426,197.71", + lp="1599.5,221.5", + pos="e,1420,193.43 2647.3,264.57 2362.3,264.82 1759.3,261.33 1553,229 1510.5,222.34 1463.7,208.27 1429.7,196.75", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -99,8 +99,8 @@ digraph { width=3.015]; "pairwise molecular interaction" -> "knowledge source" [color=blue, label="knowledge source", - lp="1714.5,221.5", - pos="e,1600.2,195.93 1846,256.91 1770.5,251.58 1685.2,242.77 1650,229 1634.7,222.99 1619.7,212.44 1607.9,202.59", + lp="1758.5,221.5", + pos="e,1611.2,195.4 2648.7,262.48 2367.5,259.19 1784.4,249.91 1694,229 1668.2,223.02 1641,210.9 1620,200.09", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -109,8 +109,8 @@ digraph { width=3.015]; "pairwise molecular interaction" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1881,221.5", - pos="e,1796.2,195.95 1858,254.6 1825.4,249.43 1796.4,241.41 1786,229 1779.4,221.14 1782.8,211.83 1789.4,203.39", + lp="1933,221.5", + pos="e,1820.1,196.34 2648.4,262.78 2385.7,260.08 1870.5,251.87 1838,229 1830.4,223.6 1825.6,214.77 1822.7,206.01", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -119,8 +119,8 @@ digraph { width=3.015]; "pairwise molecular interaction" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2090.5,221.5", - pos="e,2005.7,194.35 1979.2,247 1977.9,236.7 1977.9,223.71 1984,214 1987.5,208.55 1992,203.91 1997.2,199.98", + lp="2142.5,221.5", + pos="e,2039.4,196.19 2648.9,262.37 2432.2,259.27 2056.8,250.78 2036,229 2029.8,222.48 2030.9,213.58 2034.6,205.1", style=solid]; timepoint [color=blue, height=0.5, @@ -129,8 +129,8 @@ digraph { width=1.5346]; "pairwise molecular interaction" -> timepoint [color=blue, label=timepoint, - lp="2249,221.5", - pos="e,2226.5,196.13 2097.2,252.98 2138.6,247.38 2179.6,239.5 2197,229 2206.8,223.12 2214.9,213.7 2221.1,204.62", + lp="2303,221.5", + pos="e,2241.5,195.99 2651,260.94 2505.2,256.87 2300.5,247.85 2268,229 2258.6,223.51 2251.3,214.11 2246.1,204.94", style=solid]; "original subject" [color=blue, height=0.5, @@ -139,8 +139,8 @@ digraph { width=1.0652]; "pairwise molecular interaction" -> "original subject" [color=blue, label="original subject", - lp="2368,221.5", - pos="e,2333.2,194.93 2091.7,252.27 2177.4,242.9 2283.4,231.01 2288,229 2302.2,222.88 2315.5,212.2 2325.9,202.28", + lp="2404,221.5", + pos="e,2342.1,196 2649.1,262.18 2525.9,259.1 2368.7,250.87 2348,229 2342.3,222.96 2340.8,214.46 2341,206.18", style=solid]; "original predicate" [color=blue, height=0.5, @@ -149,124 +149,239 @@ digraph { width=1.5887]; "pairwise molecular interaction" -> "original predicate" [color=blue, label="original predicate", - lp="2505.5,221.5", - pos="e,2453.6,196.03 2090.2,252.14 2108.5,250.29 2127.3,248.5 2145,247 2176.1,244.37 2397.8,244.1 2425,229 2434.9,223.56 2442.7,214.17 \ -2448.5,204.99", + lp="2536.5,221.5", + pos="e,2460.5,196.38 2664.2,256.77 2581,251.09 2487.8,241.96 2473,229 2466.6,223.3 2463.3,214.78 2461.7,206.37", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2593,178", + pos="2589,178", width=1.0652]; "pairwise molecular interaction" -> "original object" [color=blue, label="original object", - lp="2636.5,221.5", - pos="e,2590.9,196.32 2088.8,251.94 2107.5,250.08 2126.8,248.34 2145,247 2168.8,245.26 2553.6,242.75 2573,229 2580.7,223.58 2585.4,214.74 \ -2588.3,205.98", + lp="2668.5,221.5", + pos="e,2594.3,195.96 2696.1,251.8 2662.5,246.24 2630.5,238.69 2617,229 2608.9,223.1 2602.8,214.04 2598.4,205.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2722,178", + width=2.1304]; + "pairwise molecular interaction" -> "subject category" [color=blue, + label="subject category", + lp="2789.5,221.5", + pos="e,2721,196.24 2752.1,247.77 2743.7,242.93 2735.7,236.78 2730,229 2725.3,222.49 2722.9,214.23 2721.8,206.3", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2893,178", + width=2.1304]; + "pairwise molecular interaction" -> "object category" [color=blue, + label="object category", + lp="2919.5,221.5", + pos="e,2879.7,196.09 2825.8,247.25 2833.6,241.78 2841.9,235.45 2849,229 2857.5,221.36 2866,212.2 2873.2,203.82", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3026,178", + width=1.0652]; + "pairwise molecular interaction" -> "subject closure" [color=blue, + label="subject closure", + lp="3053.5,221.5", + pos="e,3014.8,195.53 2913.6,252.83 2936.2,247.62 2959.1,240.02 2979,229 2990.3,222.76 3000.5,212.86 3008.4,203.5", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3132,178", + width=1.0652]; + "pairwise molecular interaction" -> "object closure" [color=blue, + label="object closure", + lp="3174,221.5", + pos="e,3129.7,196.09 2909.5,252.38 2998.6,242.81 3110,230.58 3112,229 3119.4,223.38 3124.1,214.61 3127,205.97", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3265,178", + width=2.1304]; + "pairwise molecular interaction" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3332.5,221.5", + pos="e,3257.3,196.02 2907.6,252.15 2925.8,250.31 2944.4,248.52 2962,247 3021.1,241.91 3176.1,257.44 3228,229 3238.1,223.5 3246.2,213.97 \ +3252.2,204.7", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3458,178", + width=2.1304]; + "pairwise molecular interaction" -> "object category closure" [color=blue, + label="object category closure", + lp="3523.5,221.5", + pos="e,3451.3,196.1 2905.4,251.93 2924.2,250.06 2943.7,248.32 2962,247 3013.3,243.32 3379.1,253.91 3424,229 3433.7,223.66 3441.1,214.28 \ +3446.6,205.09", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3648,178", + width=1.0652]; + "pairwise molecular interaction" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3696,221.5", + pos="e,3640.6,195.7 2904.5,251.85 2923.6,249.96 2943.4,248.23 2962,247 2998,244.62 3579.1,245.68 3611,229 3621.3,223.63 3629.5,213.94 \ +3635.5,204.51", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3807,178", + width=1.0652]; + "pairwise molecular interaction" -> "object namespace" [color=blue, + label="object namespace", + lp="3850,221.5", + pos="e,3799,195.74 2904.1,251.81 2923.3,249.91 2943.3,248.19 2962,247 3006.7,244.16 3728,249.1 3768,229 3778.7,223.63 3787.4,213.8 3793.8,\ +204.27", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3958,178", + width=1.0652]; + "pairwise molecular interaction" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4010,221.5", + pos="e,3949.7,195.77 2904.1,251.75 2923.3,249.86 2943.3,248.16 2962,247 3015.1,243.73 3870.4,252.46 3918,229 3928.9,223.66 3937.7,213.84 \ +3944.3,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4129,178", + width=1.0652]; + "pairwise molecular interaction" -> "object label closure" [color=blue, + label="object label closure", + lp="4175.5,221.5", + pos="e,4120.4,195.79 2903.6,251.75 2923,249.85 2943.1,248.14 2962,247 3024.5,243.23 4031.7,256.21 4088,229 4099,223.69 4108.1,213.87 \ +4114.9,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4282,178", + width=2.347]; + "pairwise molecular interaction" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4334.5,221.5", + pos="e,4275.7,196.19 2903.6,251.72 2923,249.82 2943.1,248.12 2962,247 2997.7,244.88 4217.7,246.16 4249,229 4258.6,223.76 4265.9,214.4 \ +4271.1,205.19", style=solid]; type [height=0.5, - pos="2681,178", + pos="4416,178", width=0.86659]; "pairwise molecular interaction" -> type [color=blue, label=type, - lp="2713,221.5", - pos="e,2691.3,195.46 2087.9,251.88 2106.9,250.01 2126.6,248.27 2145,247 2175.4,244.91 2670.9,250.85 2692,229 2698.2,222.6 2697.9,213.54 \ -2695.2,204.89", + lp="4433,221.5", + pos="e,4418.4,196.02 2903.6,251.7 2923,249.8 2943.1,248.11 2962,247 2982.1,245.83 4392.8,242.13 4408,229 4414.6,223.36 4417.3,214.7 4418.1,\ +206.17", style=solid]; category [height=0.5, - pos="2782,178", + pos="4517,178", width=1.4263]; "pairwise molecular interaction" -> category [color=blue, label=category, - lp="2785.5,221.5", - pos="e,2770.9,195.79 2087.9,251.85 2106.9,249.97 2126.6,248.25 2145,247 2210.2,242.59 2673.2,255.24 2733,229 2745.4,223.59 2756.2,213.48 \ -2764.6,203.76", + lp="4512.5,221.5", + pos="e,4502,195.47 2903.6,251.69 2923,249.79 2943.1,248.1 2962,247 3044.7,242.17 4374.9,256.44 4453,229 4468.6,223.54 4483.3,212.62 4494.7,\ +202.38", style=solid]; "interacting molecules category" [color=blue, height=0.5, label="ontology class", - pos="2928,178", + pos="4663,178", width=2.1304]; "pairwise molecular interaction" -> "interacting molecules category" [color=blue, label="interacting molecules category", - lp="2975,221.5", - pos="e,2901.9,194.95 2087.5,251.83 2106.6,249.95 2126.4,248.22 2145,247 2220,242.08 2747.9,246.27 2821,229 2846.3,223.03 2872.7,210.74 \ -2893,199.84", + lp="4705,221.5", + pos="e,4635.3,194.83 2903.2,251.72 2922.7,249.81 2943,248.11 2962,247 3050,241.9 4461.9,247.43 4548,229 4575.4,223.14 4604.3,210.55 4626.3,\ +199.47", style=solid]; subject [height=0.5, - pos="3095,178", + pos="4825,178", width=1.2277]; "pairwise molecular interaction" -> subject [color=blue, label=subject, - lp="3122,221.5", - pos="e,3097.3,196 2087.1,251.76 2106.3,249.87 2126.3,248.16 2145,247 2171.2,245.38 3067.3,246.17 3087,229 3093.5,223.34 3096.2,214.68 \ -3097.1,206.14", + lp="4852,221.5", + pos="e,4827.4,196.03 2903.2,251.7 2922.7,249.79 2943,248.09 2962,247 2987.8,245.53 4797.5,245.81 4817,229 4823.6,223.37 4826.3,214.71 \ +4827.1,206.18", style=solid]; id [height=0.5, - pos="3184,178", + pos="4914,178", width=0.75]; "pairwise molecular interaction" -> id [color=blue, label=id, - lp="3175,221.5", - pos="e,3178.2,195.67 2087.1,251.74 2106.3,249.85 2126.3,248.15 2145,247 2173,245.29 3127.6,242.65 3152,229 3161.6,223.64 3168.8,214.09 \ -3173.8,204.76", + lp="4905,221.5", + pos="e,4908.3,195.7 2903.2,251.69 2922.7,249.78 2943,248.09 2962,247 3015.3,243.96 4835.4,254.82 4882,229 4891.6,223.69 4898.8,214.14 \ +4903.9,204.8", style=solid]; predicate [height=0.5, - pos="3284,178", + pos="5014,178", width=1.5165]; "pairwise molecular interaction" -> predicate [color=blue, label=predicate, - lp="3260,221.5", - pos="e,3261.1,194.53 2086.6,251.77 2106,249.87 2126.1,248.15 2145,247 2260.5,239.96 3073.8,257.01 3186,229 3209.6,223.12 3233.9,210.74 \ -3252.5,199.77", + lp="4990,221.5", + pos="e,4991.1,194.59 2903.2,251.69 2922.7,249.78 2943,248.09 2962,247 3070.4,240.83 4810.6,254.86 4916,229 4939.6,223.21 4964,210.84 \ +4982.5,199.84", style=solid]; object [height=0.5, - pos="3162,91", + pos="4892,91", width=1.0832]; "pairwise molecular interaction" -> object [color=blue, label=object, - lp="3375,178", - pos="e,3199.4,96.831 2086.6,251.74 2106,249.84 2126.1,248.14 2145,247 2209,243.15 3236.8,247.9 3298,229 3323.5,221.14 3335.4,219.45 3348,\ -196 3379.7,137.24 3274.4,109.66 3209.4,98.485", + lp="5105,178", + pos="e,4929.4,96.831 2903.2,251.68 2922.7,249.77 2943,248.08 2962,247 3019.3,243.75 4973.1,245.74 5028,229 5053.5,221.23 5065.4,219.45 \ +5078,196 5109.7,137.24 5004.4,109.66 4939.4,98.485", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2192,265", + pos="3009,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2323,265", + pos="3140,265", width=2.0762]; subject -> object [label=relation, - lp="3161,134.5", - pos="e,3149.4,108.05 3108,160.61 3117.9,147.95 3131.9,130.24 3143.1,115.98"]; + lp="4891,134.5", + pos="e,4879.4,108.05 4838,160.61 4847.9,147.95 4861.9,130.24 4873.1,115.98"]; relation [height=0.5, - pos="3107,18", + pos="4837,18", width=1.2999]; - subject -> relation [pos="e,3105.7,36.188 3096.3,159.79 3098.4,132.48 3102.5,78.994 3105,46.38", + subject -> relation [pos="e,4835.7,36.188 4826.3,159.79 4828.4,132.48 4832.5,78.994 4835,46.38", style=dotted]; "pairwise molecular interaction_subject" [color=blue, height=0.5, label="molecular entity", - pos="2503,265", + pos="3320,265", width=2.4192]; "pairwise molecular interaction_id" [color=blue, height=0.5, label=string, - pos="2646,265", + pos="3463,265", width=1.0652]; "pairwise molecular interaction_predicate" [color=blue, height=0.5, label="predicate type", - pos="2780,265", + pos="3597,265", width=2.1665]; - object -> relation [pos="e,3119.8,35.54 3149.6,73.889 3142.6,64.939 3133.9,53.617 3126.1,43.584", + object -> relation [pos="e,4849.8,35.54 4879.6,73.889 4872.6,64.939 4863.9,53.617 4856.1,43.584", style=dotted]; "pairwise molecular interaction_object" [color=blue, height=0.5, label="molecular entity", - pos="2963,265", + pos="3780,265", width=2.4192]; } diff --git a/graphviz/pairwise_molecular_interaction.svg b/graphviz/pairwise_molecular_interaction.svg index d74365e25c..325a59e207 100644 --- a/graphviz/pairwise_molecular_interaction.svg +++ b/graphviz/pairwise_molecular_interaction.svg @@ -4,16 +4,16 @@ - + %3 - + pairwise molecular interaction - -pairwise molecular interaction + +pairwise molecular interaction @@ -24,8 +24,8 @@ pairwise molecular interaction->pairwise gene to gene interaction - - + + is_a @@ -37,7 +37,7 @@ pairwise molecular interaction->iri - + iri @@ -50,8 +50,8 @@ pairwise molecular interaction->name - - + + name @@ -63,8 +63,8 @@ pairwise molecular interaction->description - - + + description @@ -76,9 +76,9 @@ pairwise molecular interaction->has attribute - - -has attribute + + +has attribute @@ -89,9 +89,9 @@ pairwise molecular interaction->negated - - -negated + + +negated @@ -102,9 +102,9 @@ pairwise molecular interaction->qualifiers - - -qualifiers + + +qualifiers @@ -115,9 +115,9 @@ pairwise molecular interaction->publications - - -publications + + +publications @@ -128,9 +128,9 @@ pairwise molecular interaction->has evidence - - -has evidence + + +has evidence @@ -141,9 +141,9 @@ pairwise molecular interaction->knowledge source - - -knowledge source + + +knowledge source @@ -154,9 +154,9 @@ pairwise molecular interaction->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -167,9 +167,9 @@ pairwise molecular interaction->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -180,9 +180,9 @@ pairwise molecular interaction->timepoint - - -timepoint + + +timepoint @@ -193,9 +193,9 @@ pairwise molecular interaction->original subject - - -original subject + + +original subject @@ -206,174 +206,317 @@ pairwise molecular interaction->original predicate - - -original predicate + + +original predicate original object - -string + +string pairwise molecular interaction->original object - - -original object + + +original object - + +subject category + +ontology class + + + +pairwise molecular interaction->subject category + + +subject category + + + +object category + +ontology class + + + +pairwise molecular interaction->object category + + +object category + + + +subject closure + +string + + + +pairwise molecular interaction->subject closure + + +subject closure + + + +object closure + +string + + + +pairwise molecular interaction->object closure + + +object closure + + + +subject category closure + +ontology class + + + +pairwise molecular interaction->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +pairwise molecular interaction->object category closure + + +object category closure + + + +subject namespace + +string + + + +pairwise molecular interaction->subject namespace + + +subject namespace + + + +object namespace + +string + + + +pairwise molecular interaction->object namespace + + +object namespace + + + +subject label closure + +string + + + +pairwise molecular interaction->subject label closure + + +subject label closure + + + +object label closure + +string + + + +pairwise molecular interaction->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +pairwise molecular interaction->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + pairwise molecular interaction->type - - -type + + +type - + category - -category + +category - + pairwise molecular interaction->category - - -category + + +category - + interacting molecules category - -ontology class + +ontology class - + pairwise molecular interaction->interacting molecules category - - -interacting molecules category + + +interacting molecules category - + subject - -subject + +subject - + pairwise molecular interaction->subject - - -subject + + +subject - + id - -id + +id - + pairwise molecular interaction->id - - -id + + +id - + predicate - -predicate + +predicate - + pairwise molecular interaction->predicate - - -predicate + + +predicate - + object - -object + +object - + pairwise molecular interaction->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + pairwise molecular interaction_subject - -molecular entity + +molecular entity - + pairwise molecular interaction_id - -string + +string - + pairwise molecular interaction_predicate - -predicate type + +predicate type - + object->relation - - + + - + pairwise molecular interaction_object - -molecular entity + +molecular entity diff --git a/graphviz/population_to_population_association.gv b/graphviz/population_to_population_association.gv index 95277f84e8..d06c8578f5 100644 --- a/graphviz/population_to_population_association.gv +++ b/graphviz/population_to_population_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3016,283"]; + graph [bb="0,0,4748,283"]; node [label="\N"]; "population to population association" [height=0.5, label="population to population association", - pos="1551.4,265", + pos="2468.4,265", width=4.9648]; association [height=0.5, pos="62.394,178", width=1.7332]; "population to population association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.65 1373.1,263.77 1072.2,262.61 476.29,256.75 268.39,229 214.64,221.83 154.52,206.34 113.17,194.5"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2290,263.46 1801.2,261.67 464.11,254.47 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "population to population association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1374.6,262.3 1098.5,259.02 577.85,250.19 393.39,229 319.53,220.51 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2290.7,262.91 1822,259.76 575.24,249.55 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "population to population association" -> iri [color=blue, label=iri, - lp="519.39,221.5", - pos="e,315.01,190.17 1376.2,261.32 1124.6,256.92 673.57,246.83 511.39,229 432.29,220.3 412.55,215.53 335.39,196 331.96,195.13 328.43,\ -194.16 324.9,193.14", + lp="509.39,221.5", + pos="e,315.3,190.2 2291,262.65 1840.6,258.97 676.07,247.76 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "population to population association" -> name [color=blue, label=name, - lp="623.39,221.5", - pos="e,440.4,191.25 1375.6,261.73 1143.4,258.01 747.37,248.92 603.39,229 550.17,221.64 490.6,205.95 450.03,194.1", + lp="616.39,221.5", + pos="e,439.35,191.54 2290.4,263.02 1855.2,260.29 760.93,251.28 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "population to population association" -> description [color=blue, label=description, - lp="741.89,221.5", - pos="e,586.72,193.92 1374,262.53 1163.6,259.76 825.69,251.8 701.39,229 665.13,222.35 625.63,208.91 596.27,197.64", + lp="736.89,221.5", + pos="e,585.45,194.14 2289.8,263.63 1871.1,262.3 849.91,256.29 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "population to population association" -> "has attribute" [color=blue, label="has attribute", - lp="884.39,221.5", - pos="e,726.75,192.68 1376.5,261.25 1199,257.42 936.63,248.59 837.39,229 802.18,222.05 763.89,208.03 736.11,196.6", + lp="882.39,221.5", + pos="e,725.98,192.82 2290,263.43 1896,261.69 975.02,254.89 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "population to population association" -> negated [color=blue, label=negated, - lp="1033.4,221.5", - pos="e,847.79,190.35 1377.8,260.61 1269.9,256.59 1128.5,247.87 1004.4,229 953.22,221.22 895.96,205.22 857.6,193.4", + lp="1038.4,221.5", + pos="e,847.59,190.46 2289.6,264.31 1956.2,264.12 1251.6,259.91 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "population to population association" -> qualifiers [color=blue, label=qualifiers, - lp="1161.9,221.5", - pos="e,995.33,193.25 1386.9,257.94 1308.2,253.13 1212.9,244.49 1128.4,229 1086.2,221.27 1039.5,207.56 1005.1,196.45", + lp="1178.9,221.5", + pos="e,996.68,193.07 2289.7,264.35 1981.1,264.09 1360.7,259.62 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "population to population association" -> publications [color=blue, label=publications, - lp="1293.4,221.5", - pos="e,1144.2,193.34 1407.7,254.22 1357.2,248.98 1300.4,241.02 1249.4,229 1216.5,221.24 1180.6,208.09 1153.7,197.22", + lp="1326.4,221.5", + pos="e,1148.1,192.71 2289.6,264.29 2007.2,263.81 1470.8,258.82 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.0943]; "population to population association" -> "has evidence" [color=blue, label="has evidence", - lp="1424.9,221.5", - pos="e,1297.3,194.68 1460.2,249.51 1433.5,244.21 1404.5,237.4 1378.4,229 1353.8,221.08 1327.4,209.32 1306.5,199.19", + lp="1480.9,221.5", + pos="e,1305.9,193.61 2290.2,263.48 2039.1,261.8 1593.7,255.1 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=3.015]; "population to population association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1547.9,221.5", - pos="e,1470.8,196.34 1506.2,247.43 1497.7,242.58 1489.5,236.51 1483.4,229 1478.1,222.52 1474.8,214.16 1472.8,206.15", + lp="1635.9,221.5", + pos="e,1495.5,195.59 2293.9,261.07 2052.6,256.44 1639.2,246.12 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -120,9 +120,8 @@ digraph { width=3.015]; "population to population association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1730.4,221.5", - pos="e,1670.7,195.19 1581.4,247.25 1591.3,241.57 1602.4,235.12 1612.4,229 1622.8,222.63 1624.8,220.1 1635.4,214 1643.8,209.16 1652.9,\ -204.28 1661.7,199.76", + lp="1807.4,221.5", + pos="e,1702.1,196.41 2292.9,261.41 2076.3,257.39 1733.7,248.07 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -131,9 +130,8 @@ digraph { width=3.015]; "population to population association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1954.9,221.5", - pos="e,1893.7,194.43 1683.1,252.78 1739.8,246.79 1799.1,238.66 1825.4,229 1836.8,224.79 1837.5,219.55 1848.4,214 1859.7,208.22 1872.2,\ -202.83 1884.2,198.09", + lp="2015.9,221.5", + pos="e,1918.7,195.97 2299.8,259 2140.1,253.41 1922.8,243.25 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", style=solid]; timepoint [color=blue, height=0.5, @@ -142,9 +140,8 @@ digraph { width=1.5346]; "population to population association" -> timepoint [color=blue, label=timepoint, - lp="2118.4,221.5", - pos="e,2104.5,195.18 1676.2,252.11 1697.3,250.27 1719,248.49 1739.4,247 1810.9,241.77 1994.7,255.27 2061.4,229 2069.3,225.87 2084,213.73 \ -2096.8,202.2", + lp="2171.4,221.5", + pos="e,2121.9,196.47 2315.9,255.58 2235.6,249.79 2150.8,240.98 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", style=solid]; "original subject" [color=blue, height=0.5, @@ -153,9 +150,8 @@ digraph { width=1.0652]; "population to population association" -> "original subject" [color=blue, label="original subject", - lp="2233.4,221.5", - pos="e,2211.3,192.7 1675.2,251.97 1696.6,250.13 1718.6,248.39 1739.4,247 1831.5,240.84 2066.5,257.21 2154.4,229 2166,225.27 2167.1,220.57 \ -2177.4,214 2185.6,208.79 2194.4,203.21 2202.7,198.07", + lp="2270.4,221.5", + pos="e,2219.6,194.92 2303.4,258.03 2263.1,252.96 2227.6,244.14 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", style=solid]; "original predicate" [color=blue, height=0.5, @@ -164,9 +160,8 @@ digraph { width=1.5887]; "population to population association" -> "original predicate" [color=blue, label="original predicate", - lp="2374.9,221.5", - pos="e,2330.8,195.49 1673.9,251.89 1695.7,250.03 1718.2,248.3 1739.4,247 1800.4,243.25 2232.4,251.23 2289.4,229 2297.1,225.98 2311.2,\ -213.98 2323.5,202.49", + lp="2397.9,221.5", + pos="e,2336.3,195.76 2379.4,249.38 2358.7,244.13 2340.9,237.37 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", style=solid]; "original object" [color=blue, height=0.5, @@ -175,88 +170,206 @@ digraph { width=1.0652]; "population to population association" -> "original object" [color=blue, label="original object", - lp="2503.9,221.5", - pos="e,2458.6,196.43 1673.4,251.81 1695.4,249.95 1718,248.24 1739.4,247 1778.2,244.75 2407.1,250.68 2439.4,229 2447.3,223.7 2452.4,214.88 \ -2455.6,206.12", + lp="2516.9,221.5", + pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2594.4,178", + width=2.1304]; + "population to population association" -> "subject category" [color=blue, + label="subject category", + lp="2642.9,221.5", + pos="e,2590.6,196.4 2540.7,248.46 2552.2,243.62 2563.3,237.29 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2765.4,178", + width=2.1304]; + "population to population association" -> "object category" [color=blue, + label="object category", + lp="2785.9,221.5", + pos="e,2750.6,195.73 2617.4,255.05 2647.8,249.69 2678.8,241.47 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="2898.4,178", + width=1.0652]; + "population to population association" -> "subject closure" [color=blue, + label="subject closure", + lp="2921.9,221.5", + pos="e,2886,195.51 2596.1,252.38 2704.9,242.45 2843.9,229.66 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="2998.4,178", + width=1.0652]; + "population to population association" -> "object closure" [color=blue, + label="object closure", + lp="3042.4,221.5", + pos="e,2997,196.23 2593.2,252.1 2614.3,250.27 2636,248.49 2656.4,247 2692.4,244.38 2951.5,250.54 2980.4,229 2987.7,223.53 2992.1,214.8 \ +2994.7,206.14", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3131.4,178", + width=2.1304]; + "population to population association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3200.9,221.5", + pos="e,3124.4,196.11 2592,251.95 2613.4,250.11 2635.5,248.37 2656.4,247 2705.2,243.8 3053.5,252.48 3096.4,229 3106.2,223.66 3113.8,214.29 \ +3119.4,205.09", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3323.4,178", + width=2.1304]; + "population to population association" -> "object category closure" [color=blue, + label="object category closure", + lp="3390.9,221.5", + pos="e,3317.7,196.1 2590.7,251.84 2612.5,249.98 2635.1,248.26 2656.4,247 2691.7,244.91 3261.8,246.63 3292.4,229 3301.6,223.71 3308.4,\ +214.47 3313.3,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3513.4,178", + width=1.0652]; + "population to population association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3563.4,221.5", + pos="e,3506.4,196.19 2589.9,251.79 2612,249.92 2634.9,248.21 2656.4,247 2702,244.44 3438.1,250.54 3478.4,229 3488.2,223.75 3495.9,214.4 \ +3501.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3672.4,178", + width=1.0652]; + "population to population association" -> "object namespace" [color=blue, + label="object namespace", + lp="3716.4,221.5", + pos="e,3665,195.73 2589.7,251.75 2611.8,249.87 2634.8,248.17 2656.4,247 2710.7,244.05 3587,253.93 3635.4,229 3645.7,223.67 3653.9,213.99 \ +3659.9,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3823.4,178", + width=1.0652]; + "population to population association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="3876.4,221.5", + pos="e,3815.4,195.77 2589.4,251.72 2611.7,249.85 2634.7,248.15 2656.4,247 2687.7,245.34 3756.3,242.97 3784.4,229 3795.1,223.66 3803.8,\ +213.84 3810.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="3994.4,178", + width=1.0652]; + "population to population association" -> "object label closure" [color=blue, + label="object label closure", + lp="4041.9,221.5", + pos="e,3986.1,195.79 2589.2,251.71 2611.5,249.82 2634.6,248.13 2656.4,247 2692.4,245.12 3922,244.85 3954.4,229 3965.3,223.69 3974.1,213.87 \ +3980.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4147.4,178", + width=2.347]; + "population to population association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4200.9,221.5", + pos="e,4141.4,196.18 2588.9,251.7 2611.3,249.81 2634.5,248.12 2656.4,247 2696.9,244.92 4080,248.68 4115.4,229 4124.9,223.75 4131.9,214.39 \ +4137,205.18", style=solid]; type [height=0.5, - pos="2549.4,178", + pos="4281.4,178", width=0.86659]; "population to population association" -> type [color=blue, label=type, - lp="2581.4,221.5", - pos="e,2559.3,195.51 1672.9,251.79 1695,249.92 1717.9,248.21 1739.4,247 1762.1,245.72 2543.5,245.29 2559.4,229 2565.6,222.66 2565.4,213.61 \ -2562.9,204.95", + lp="4299.4,221.5", + pos="e,4284.1,195.98 2588.9,251.68 2611.3,249.79 2634.5,248.11 2656.4,247 2678.8,245.86 4257.5,243.84 4274.4,229 4280.9,223.32 4283.4,\ +214.65 4284.1,206.12", style=solid]; category [height=0.5, - pos="2650.4,178", + pos="4382.4,178", width=1.4263]; "population to population association" -> category [color=blue, label=category, - lp="2654.9,221.5", - pos="e,2639.3,195.84 1672.9,251.77 1695,249.9 1717.9,248.2 1739.4,247 1787.2,244.34 2557.4,248.01 2601.4,229 2613.8,223.65 2624.6,213.54 \ -2632.9,203.81", + lp="4377.9,221.5", + pos="e,4367.7,195.48 2588.9,251.68 2611.3,249.79 2634.5,248.1 2656.4,247 2702.5,244.67 4275.9,244.44 4319.4,229 4334.6,223.59 4349,212.83 \ +4360.1,202.68", style=solid]; subject [height=0.5, - pos="2764.4,178", + pos="4496.4,178", width=1.2277]; "population to population association" -> subject [color=blue, label=subject, - lp="2747.4,221.5", - pos="e,2747.4,194.73 1672.7,251.76 1694.8,249.88 1717.8,248.18 1739.4,247 1792.2,244.12 2640,244.95 2690.4,229 2708.4,223.3 2726,211.72 \ -2739.5,201.13", + lp="4473.4,221.5", + pos="e,4477.7,194.32 2588.9,251.66 2611.3,249.78 2634.5,248.1 2656.4,247 2753.9,242.1 4319.5,255.62 4413.4,229 4433.6,223.29 4453.7,211.3 \ +4469.2,200.49", style=solid]; object [height=0.5, - pos="2807.4,91", + pos="4539.4,91", width=1.0832]; "population to population association" -> object [color=blue, label=object, - lp="2850.4,178", - pos="e,2820.8,108.09 1672.4,251.75 1694.7,249.87 1717.7,248.17 1739.4,247 1797,243.9 2723.3,248.97 2777.4,229 2819.9,213.32 2825.1,186.96 \ -2830.4,142 2831.2,135.38 2832.3,133.39 2830.4,127 2829.4,123.55 2827.9,120.13 2826.1,116.85", + lp="4583.4,178", + pos="e,4552.8,108.09 2588.6,251.68 2611.1,249.78 2634.5,248.1 2656.4,247 2707.6,244.44 4454.6,244.95 4503.4,229 4527.3,221.18 4535.3,\ +216.87 4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,\ +116.85", style=solid]; predicate [height=0.5, - pos="2961.4,178", + pos="4693.4,178", width=1.5165]; "population to population association" -> predicate [color=blue, label=predicate, - lp="2934.4,221.5", - pos="e,2937.6,194.3 1672.4,251.73 1694.7,249.85 1717.7,248.15 1739.4,247 1863.6,240.4 2737.4,257.83 2858.4,229 2883.3,223.07 2909.1,210.48 \ -2928.7,199.41", + lp="4666.4,221.5", + pos="e,4669.6,194.35 2588.6,251.67 2611.1,249.78 2634.5,248.09 2656.4,247 2763.7,241.66 4485.8,253.56 4590.4,229 4615.3,223.16 4641.2,\ +210.56 4660.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1786.4,265", + pos="2703.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1917.4,265", + pos="2834.4,265", width=2.0762]; subject -> object [label=relation, - lp="2802.4,134.5", - pos="e,2789.5,107.23 2765.5,159.55 2766.7,149.57 2769.2,137.07 2774.4,127 2776.6,122.68 2779.5,118.52 2782.7,114.66"]; + lp="4534.4,134.5", + pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; relation [height=0.5, - pos="2752.4,18", + pos="4484.4,18", width=1.2999]; - subject -> relation [pos="e,2753.7,36.188 2763.1,159.79 2761,132.48 2757,78.994 2754.5,46.38", + subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", style=dotted]; "population to population association_subject" [color=blue, height=0.5, label="population of individual organisms", - pos="2181.4,265", + pos="3098.4,265", width=4.7662]; - object -> relation [pos="e,2765.2,35.54 2794.9,73.889 2788,64.939 2779.2,53.617 2771.4,43.584", + object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", style=dotted]; "population to population association_object" [color=blue, height=0.5, label="population of individual organisms", - pos="2542.4,265", + pos="3459.4,265", width=4.7662]; "population to population association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2810.4,265", + pos="3727.4,265", width=2.1665]; } diff --git a/graphviz/population_to_population_association.svg b/graphviz/population_to_population_association.svg index e1a54530f8..279cea5d16 100644 --- a/graphviz/population_to_population_association.svg +++ b/graphviz/population_to_population_association.svg @@ -4,16 +4,16 @@ - + %3 - + population to population association - -population to population association + +population to population association @@ -24,9 +24,9 @@ population to population association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ population to population association->id - - -id + + +id @@ -50,9 +50,9 @@ population to population association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ population to population association->name - - -name + + +name @@ -76,9 +76,9 @@ population to population association->description - - -description + + +description @@ -89,9 +89,9 @@ population to population association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ population to population association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ population to population association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ population to population association->publications - - -publications + + +publications @@ -141,9 +141,9 @@ population to population association->has evidence - - -has evidence + + +has evidence @@ -154,9 +154,9 @@ population to population association->knowledge source - - -knowledge source + + +knowledge source @@ -167,9 +167,9 @@ population to population association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -180,9 +180,9 @@ population to population association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -193,9 +193,9 @@ population to population association->timepoint - - -timepoint + + +timepoint @@ -206,9 +206,9 @@ population to population association->original subject - - -original subject + + +original subject @@ -219,9 +219,9 @@ population to population association->original predicate - - -original predicate + + +original predicate @@ -232,129 +232,272 @@ population to population association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +population to population association->subject category + + +subject category + + + +object category + +ontology class + + + +population to population association->object category + + +object category + + + +subject closure + +string + + + +population to population association->subject closure + + +subject closure + + + +object closure + +string + + + +population to population association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +population to population association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +population to population association->object category closure + + +object category closure + + + +subject namespace + +string + + + +population to population association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +population to population association->object namespace + + +object namespace + + + +subject label closure + +string + + + +population to population association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +population to population association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +population to population association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + population to population association->type - - -type + + +type - + category - -category + +category - + population to population association->category - - -category + + +category - + subject - -subject + +subject - + population to population association->subject - - -subject + + +subject - + object - -object + +object - + population to population association->object - - -object + + +object - + predicate - -predicate + +predicate - + population to population association->predicate - - -predicate + + +predicate - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + population to population association_subject - -population of individual organisms + +population of individual organisms - + object->relation - - + + - + population to population association_object - -population of individual organisms + +population of individual organisms - + population to population association_predicate - -predicate type + +predicate type diff --git a/graphviz/reaction_to_catalyst_association.gv b/graphviz/reaction_to_catalyst_association.gv index f0a8925b9e..7ad0ab996b 100644 --- a/graphviz/reaction_to_catalyst_association.gv +++ b/graphviz/reaction_to_catalyst_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3851.6,283"]; + graph [bb="0,0,5574.6,283"]; node [label="\N"]; "reaction to catalyst association" [height=0.5, label="reaction to catalyst association", - pos="2026.6,265", + pos="2919.6,265", width=4.3149]; "reaction to participant association" [height=0.5, pos="169.63,178", width=4.7121]; "reaction to catalyst association" -> "reaction to participant association" [label=is_a, - lp="496.63,221.5", - pos="e,245.81,194.14 1871.9,263.16 1535.9,260.91 748.66,253.15 482.63,229 405.38,221.99 318.31,207.54 255.65,195.97"]; + lp="495.63,221.5", + pos="e,244.91,194.2 2765.2,263.08 2264.8,259.93 707.65,248.63 481.63,229 404.5,222.3 317.58,207.79 255.11,196.12"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "reaction to catalyst association" -> id [color=blue, label=id, - lp="614.63,221.5", - pos="e,424.62,190.01 1871.6,263.58 1556,262.16 848.32,255.98 607.63,229 533.75,220.72 515.3,215.79 443.63,196 440.52,195.14 437.33,194.18 \ -434.13,193.17", + lp="612.63,221.5", + pos="e,424.62,190 2764.6,263.33 2280.7,260.99 818.46,252.08 605.63,229 532.58,221.08 514.44,215.65 443.63,196 440.53,195.14 437.33,194.17 \ +434.13,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "reaction to catalyst association" -> iri [color=blue, label=iri, - lp="733.63,221.5", - pos="e,529.25,190.17 1872.2,262.91 1577.1,260.33 943.36,252.19 725.63,229 646.5,220.57 626.79,215.53 549.63,196 546.21,195.13 542.67,\ -194.16 539.14,193.14", + lp="729.63,221.5", + pos="e,529.53,190.23 2765,263.09 2298.2,260.13 922.84,249.74 721.63,229 644.21,221.02 625.05,215.26 549.63,196 546.26,195.14 542.78,194.18 \ +539.29,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "reaction to catalyst association" -> name [color=blue, label=name, - lp="846.63,221.5", - pos="e,655.23,191.05 1872,263.23 1594.9,261.23 1024.1,254.11 826.63,229 770.45,221.86 707.44,205.84 665.02,193.85", + lp="840.63,221.5", + pos="e,654.44,191.28 2764.7,263.35 2312.1,261.19 1011.3,252.93 820.63,229 766.24,222.17 705.38,206.24 664.21,194.18", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "reaction to catalyst association" -> description [color=blue, label=description, - lp="977.13,221.5", - pos="e,804.72,193.5 1871.4,263.83 1614.5,262.74 1111.8,256.96 936.63,229 894.52,222.28 848.16,208.29 814.35,196.82", + lp="968.13,221.5", + pos="e,802.89,193.79 2764.4,263.79 2327.4,262.83 1106.6,257.6 927.63,229 887.86,222.64 844.32,208.8 812.4,197.28", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "reaction to catalyst association" -> "has attribute" [color=blue, label="has attribute", - lp="1131.6,221.5", - pos="e,945.07,191.59 1872.4,262.8 1645.2,260.27 1231.6,252.49 1084.6,229 1039.6,221.8 989.67,206.69 954.9,194.95", + lp="1123.6,221.5", + pos="e,943.71,191.9 2764.7,263.48 2350.9,261.76 1240.7,254.77 1076.6,229 1033.8,222.27 986.59,207.28 953.5,195.45", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "reaction to catalyst association" -> predicate [color=blue, label=predicate, - lp="1286.6,221.5", - pos="e,1102.4,193.06 1875.3,260.87 1684.8,256.29 1368.5,246.35 1252.6,229 1204.5,221.79 1151,207.51 1112.4,196.05", + lp="1282.6,221.5", + pos="e,1101.1,193.25 2765.3,262.85 2380,259.67 1396,249.64 1248.6,229 1201.2,222.36 1148.6,207.95 1110.8,196.3", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "reaction to catalyst association" -> negated [color=blue, label=negated, - lp="1422.6,221.5", - pos="e,1235.9,190.33 1871.7,263.24 1743.1,260.75 1555.6,252.79 1393.6,229 1342,221.42 1284.3,205.31 1245.7,193.41", + lp="1424.6,221.5", + pos="e,1235.5,190.46 2764.2,264.57 2430.9,265.12 1656.5,262.58 1395.6,229 1343.1,222.23 1284.3,205.81 1245.4,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "reaction to catalyst association" -> qualifiers [color=blue, label=qualifiers, - lp="1553.1,221.5", - pos="e,1383.9,193.28 1874,261.66 1772.8,258.1 1637.5,249.49 1519.6,229 1476.4,221.48 1428.5,207.6 1393.4,196.37", + lp="1563.1,221.5", + pos="e,1384.4,193.2 2764.1,264.7 2452.9,265.34 1763.6,262.73 1529.6,229 1482.9,222.26 1431.2,207.87 1394,196.25", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "reaction to catalyst association" -> publications [color=blue, label=publications, - lp="1686.6,221.5", - pos="e,1533.1,193.32 1879.5,259.05 1807.4,254.49 1719.8,245.75 1642.6,229 1608.1,221.52 1570.5,208.14 1542.5,197.11", + lp="1708.6,221.5", + pos="e,1535.4,192.85 2764.2,264.82 2476.6,265.48 1871.6,262.63 1664.6,229 1623.3,222.28 1577.8,207.95 1545.1,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "reaction to catalyst association" -> "has evidence" [color=blue, label="has evidence", - lp="1826.1,221.5", - pos="e,1687.5,194.37 1908.9,253.23 1867.6,247.9 1821.2,240.13 1779.6,229 1751.3,221.39 1720.6,209.08 1696.9,198.58", + lp="1867.1,221.5", + pos="e,1693.6,193.63 2764.4,264.06 2505.7,263.33 1997.4,258.08 1820.6,229 1780.2,222.35 1735.9,208.52 1703.3,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "reaction to catalyst association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1955.1,221.5", - pos="e,1865,196.24 1935.1,250.34 1919.4,245.3 1903.8,238.42 1890.6,229 1882.1,222.9 1875.2,213.84 1869.9,205.1", + lp="2022.1,221.5", + pos="e,1883.2,195.61 2766.4,261.99 2514.6,258.15 2033.6,248.39 1957.6,229 1934.5,223.1 1910.6,211.34 1891.9,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "reaction to catalyst association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2122.6,221.5", - pos="e,2048.3,194.65 2022.8,246.59 2021.6,236.37 2021.8,223.63 2027.6,214 2030.8,208.82 2035,204.35 2039.8,200.52", + lp="2193.6,221.5", + pos="e,2089.6,196.33 2765.6,262.52 2534.6,259.59 2122.7,251.25 2098.6,229 2092.5,223.32 2090.1,214.91 2089.5,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "reaction to catalyst association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2347.1,221.5", - pos="e,2284,194.64 2134.3,251.95 2162.1,246.78 2191.5,239.43 2217.6,229 2229,224.48 2229.8,219.64 2240.6,214 2251.4,208.42 2263.2,203.13 \ -2274.5,198.44", + lp="2402.1,221.5", + pos="e,2305.8,195.87 2768.5,260.67 2589,255.97 2311.7,245.99 2295.6,229 2288.5,221.43 2292,212.05 2298.8,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "reaction to catalyst association" -> timepoint [color=blue, label=timepoint, - lp="2509.6,221.5", - pos="e,2493.7,195.41 2136.2,252.18 2154.7,250.34 2173.7,248.54 2191.6,247 2249.8,242.01 2399.9,251.66 2453.6,229 2461.1,225.87 2474.4,\ -214.06 2486.2,202.71", + lp="2556.6,221.5", + pos="e,2509,196.43 2772.1,259.29 2666.9,254.54 2540.8,245.49 2521.6,229 2515.1,223.36 2511.8,214.85 2510.2,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "reaction to catalyst association" -> "original subject" [color=blue, label="original subject", - lp="2624.6,221.5", - pos="e,2600.5,193.27 2134.8,252.04 2153.8,250.18 2173.3,248.41 2191.6,247 2270.4,240.95 2471.6,253.8 2546.6,229 2548,228.56 2571.7,212.71 \ -2592.1,198.98", + lp="2654.6,221.5", + pos="e,2605.9,194.82 2779,257.26 2698.5,251.91 2611.2,242.98 2598.6,229 2592,221.56 2594.6,211.86 2600,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,9 +170,8 @@ digraph { width=1.5887]; "reaction to catalyst association" -> "original predicate" [color=blue, label="original predicate", - lp="2765.1,221.5", - pos="e,2720.3,195.48 2133.9,251.91 2153.1,250.04 2173,248.3 2191.6,247 2246,243.21 2631.3,249.81 2681.6,229 2688.9,225.98 2701.8,214.17 \ -2713.2,202.8", + lp="2781.1,221.5", + pos="e,2721.8,195.8 2790.9,254.86 2757.7,249.7 2728.3,241.63 2717.6,229 2711.8,222.05 2713.1,213.06 2716.9,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -184,107 +180,224 @@ digraph { width=1.0652]; "reaction to catalyst association" -> "original object" [color=blue, label="original object", - lp="2895.1,221.5", - pos="e,2848.3,196.32 2133,251.86 2152.5,249.97 2172.7,248.24 2191.6,247 2227.1,244.68 2802.8,249.86 2831.6,229 2839,223.63 2843.4,214.92 \ -2846,206.26", + lp="2905.1,221.5", + pos="e,2847.1,196.07 2874,247.64 2866,242.81 2858.7,236.69 2853.6,229 2849.2,222.32 2847.5,214 2847,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2982.6,178", + width=2.1304]; + "reaction to catalyst association" -> "subject category" [color=blue, + label="subject category", + lp="3029.1,221.5", + pos="e,2977.2,196.22 2943.1,247.1 2949.3,241.81 2955.7,235.61 2960.6,229 2965.9,221.97 2970.2,213.49 2973.6,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3153.6,178", + width=2.1304]; + "reaction to catalyst association" -> "object category" [color=blue, + label="object category", + lp="3172.1,221.5", + pos="e,3137.6,195.91 3023.4,251.53 3046.9,246.41 3071.2,239.18 3092.6,229 3106.2,222.54 3119.4,212.41 3130,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3286.6,178", + width=1.0652]; + "reaction to catalyst association" -> "subject closure" [color=blue, + label="subject closure", + lp="3309.1,221.5", + pos="e,3273.6,195.42 3030.4,252.37 3118.2,243.03 3226.9,231.13 3231.6,229 3244.8,223.04 3257,212.72 3266.5,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3386.6,178", + width=1.0652]; + "reaction to catalyst association" -> "object closure" [color=blue, + label="object closure", + lp="3429.6,221.5", + pos="e,3384.8,196.23 3028.7,252.15 3047.4,250.3 3066.6,248.51 3084.6,247 3116,244.38 3342.3,247.7 3367.6,229 3375,223.53 3379.6,214.8 \ +3382.3,206.14", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3519.6,178", + width=2.1304]; + "reaction to catalyst association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3588.1,221.5", + pos="e,3512.3,196.11 3027.4,252 3046.4,250.13 3066.1,248.37 3084.6,247 3128.9,243.72 3444.6,250.12 3483.6,229 3493.6,223.6 3501.5,214.09 \ +3507.3,204.8", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3711.6,178", + width=2.1304]; + "reaction to catalyst association" -> "object category closure" [color=blue, + label="object category closure", + lp="3779.1,221.5", + pos="e,3705.6,196.11 3026.5,251.85 3045.8,249.98 3065.8,248.25 3084.6,247 3117.6,244.8 3650.9,245.31 3679.6,229 3689,223.66 3696.1,214.29 \ +3701.2,205.09", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3901.6,178", + width=1.0652]; + "reaction to catalyst association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3951.6,221.5", + pos="e,3894.6,196.18 3025.6,251.82 3045.2,249.93 3065.5,248.2 3084.6,247 3128,244.27 3828.3,249.51 3866.6,229 3876.4,223.75 3884.1,214.39 \ +3889.7,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4060.6,178", + width=1.0652]; + "reaction to catalyst association" -> "object namespace" [color=blue, + label="object namespace", + lp="4104.6,221.5", + pos="e,4053.3,195.73 3025.6,251.76 3045.2,249.87 3065.5,248.17 3084.6,247 3136.7,243.82 3977.3,252.93 4023.6,229 4034,223.67 4042.1,213.99 \ +4048.2,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4211.6,178", + width=1.0652]; + "reaction to catalyst association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4264.6,221.5", + pos="e,4203.6,195.77 3025.2,251.76 3044.9,249.86 3065.4,248.15 3084.6,247 3145,243.4 4118.5,255.97 4172.6,229 4183.3,223.66 4192,213.84 \ +4198.4,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4382.6,178", + width=1.0652]; + "reaction to catalyst association" -> "object label closure" [color=blue, + label="object label closure", + lp="4430.1,221.5", + pos="e,4374.3,195.79 3025.1,251.73 3044.9,249.83 3065.4,248.13 3084.6,247 3119.5,244.96 4311.2,244.36 4342.6,229 4353.5,223.69 4362.3,\ +213.87 4368.9,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4526.6,178", + width=2.347]; + "reaction to catalyst association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4586.1,221.5", + pos="e,4523.7,196.01 3025.1,251.7 3044.9,249.81 3065.4,248.11 3084.6,247 3124,244.73 4470.6,250.48 4503.6,229 4511.8,223.7 4517.1,214.72 \ +4520.5,205.82", style=solid]; type [height=0.5, - pos="2937.6,178", + pos="4660.6,178", width=0.86659]; "reaction to catalyst association" -> type [color=blue, label=type, - lp="2971.6,221.5", - pos="e,2948.6,194.96 2132.6,251.83 2152.2,249.94 2172.5,248.21 2191.6,247 2212.7,245.67 2935.9,244.09 2950.6,229 2957.1,222.4 2956.2,\ -213.04 2952.9,204.2", + lp="4682.6,221.5", + pos="e,4665.7,196.18 3024.7,251.73 3044.6,249.81 3065.2,248.11 3084.6,247 3106.5,245.75 4644.1,244.4 4659.6,229 4665.6,223.09 4667.2,\ +214.51 4666.9,206.12", style=solid]; category [height=0.5, - pos="3038.6,178", + pos="4761.6,178", width=1.4263]; "reaction to catalyst association" -> category [color=blue, label=category, - lp="3045.1,221.5", - pos="e,3028.2,195.82 2132.6,251.81 2152.2,249.92 2172.5,248.2 2191.6,247 2236,244.22 2951,247.1 2991.6,229 3003.7,223.62 3014.1,213.51 \ -3022.1,203.78", + lp="4760.1,221.5", + pos="e,4748,195.46 3024.7,251.72 3044.6,249.81 3065.2,248.11 3084.6,247 3129.5,244.44 4660.5,244.71 4702.6,229 4717.2,223.56 4730.7,212.8 \ +4741.1,202.65", style=solid]; stoichiometry [color=blue, height=0.5, label=integer, - pos="3152.6,178", + pos="4875.6,178", width=1.2277]; "reaction to catalyst association" -> stoichiometry [color=blue, label=stoichiometry, - lp="3160.1,221.5", - pos="e,3136.2,194.72 2132.6,251.78 2152.2,249.89 2172.5,248.18 2191.6,247 2240.9,243.97 3033.6,244.24 3080.6,229 3098.1,223.34 3115.1,\ -211.92 3128.2,201.42", + lp="4878.1,221.5", + pos="e,4857.4,194.55 3024.7,251.71 3044.6,249.8 3065.2,248.1 3084.6,247 3179.5,241.62 4704.4,255.69 4795.6,229 4815.1,223.31 4834.4,211.44 \ +4849.2,200.7", style=solid]; "reaction direction" [color=blue, height=0.5, label=ReactionDirectionEnum, - pos="3336.6,178", + pos="5059.6,178", width=3.3761]; "reaction to catalyst association" -> "reaction direction" [color=blue, label="reaction direction", - lp="3326.1,221.5", - pos="e,3305.3,195.52 2132.2,251.78 2151.9,249.88 2172.4,248.16 2191.6,247 2305,240.17 3102.4,251.77 3213.6,229 3242.2,223.15 3272.6,210.86 \ -3296,199.94", + lp="5046.1,221.5", + pos="e,5027.2,195.47 3024.7,251.7 3044.6,249.79 3065.2,248.09 3084.6,247 3187.1,241.24 4830.9,248.49 4931.6,229 4961.5,223.22 4993.4,\ +210.79 5017.9,199.76", style=solid]; "reaction side" [color=blue, height=0.5, label=ReactionSideEnum, - pos="3574.6,178", + pos="5297.6,178", width=2.7442]; "reaction to catalyst association" -> "reaction side" [color=blue, label="reaction side", - lp="3511.1,221.5", - pos="e,3531.4,194.29 2132.1,251.74 2151.9,249.84 2172.4,248.13 2191.6,247 2325,239.15 3261.4,247.94 3393.6,229 3437.6,222.71 3486,208.96 \ -3521.7,197.47", + lp="5232.1,221.5", + pos="e,5254.1,194.25 3024.7,251.68 3044.6,249.78 3065.2,248.08 3084.6,247 3309.7,234.43 4890.3,259.81 5113.6,229 5158.4,222.82 5207.8,\ +208.99 5244.2,197.44", style=solid]; subject [height=0.5, - pos="3735.6,178", + pos="5458.6,178", width=1.2277]; "reaction to catalyst association" -> subject [color=blue, label=subject, - lp="3655.6,221.5", - pos="e,3704.5,190.84 2132.1,251.71 2151.9,249.81 2172.4,248.12 2191.6,247 2343.6,238.19 3410.9,250.2 3561.6,229 3608.2,222.45 3659.8,\ -206.46 3694.7,194.31", + lp="5377.6,221.5", + pos="e,5427.4,190.79 3024.7,251.67 3044.6,249.77 3065.2,248.08 3084.6,247 3328.5,233.47 5040.6,261.91 5282.6,229 5330.1,222.54 5382.7,\ +206.34 5418,194.12", style=solid]; object [height=0.5, - pos="3778.6,91", + pos="5501.6,91", width=1.0832]; "reaction to catalyst association" -> object [color=blue, label=object, - lp="3829.6,178", - pos="e,3792,108.09 2131.7,251.73 2151.6,249.82 2172.2,248.11 2191.6,247 2357.4,237.48 3521.8,255.62 3685.6,229 3733.1,221.29 3755.9,231.22 \ -3788.6,196 3809.9,173.13 3810.6,156.9 3801.6,127 3800.6,123.55 3799.1,120.13 3797.4,116.85", + lp="5552.6,178", + pos="e,5515,108.09 3024.7,251.67 3044.6,249.76 3065.2,248.07 3084.6,247 3213.5,239.88 5280.2,249.24 5407.6,229 5455.5,221.39 5478.6,231.49 \ +5511.6,196 5532.9,173.16 5533.6,156.9 5524.6,127 5523.6,123.55 5522.1,120.13 5520.4,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2238.6,265", + pos="3131.6,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2369.6,265", + pos="3262.6,265", width=2.0762]; subject -> object [label=relation, - lp="3773.6,134.5", - pos="e,3760.7,107.23 3736.7,159.55 3737.9,149.57 3740.4,137.07 3745.6,127 3747.9,122.68 3750.8,118.52 3754,114.66"]; + lp="5496.6,134.5", + pos="e,5483.7,107.23 5459.7,159.55 5460.9,149.57 5463.4,137.07 5468.6,127 5470.9,122.68 5473.8,118.52 5477,114.66"]; relation [height=0.5, - pos="3723.6,18", + pos="5446.6,18", width=1.2999]; - subject -> relation [pos="e,3724.9,36.188 3734.3,159.79 3732.3,132.48 3728.2,78.994 3725.7,46.38", + subject -> relation [pos="e,5447.9,36.188 5457.3,159.79 5455.3,132.48 5451.2,78.994 5448.7,46.38", style=dotted]; "reaction to participant association_subject" [color=blue, height=0.5, label="molecular entity", - pos="2549.6,265", + pos="3442.6,265", width=2.4192]; - object -> relation [pos="e,3736.4,35.54 3766.2,73.889 3759.2,64.939 3750.5,53.617 3742.7,43.584", + object -> relation [pos="e,5459.4,35.54 5489.2,73.889 5482.2,64.939 5473.5,53.617 5465.7,43.584", style=dotted]; "reaction to catalyst association_object" [color=blue, height=0.5, label="gene or gene product", - pos="2765.6,265", + pos="3658.6,265", width=3.0692]; } diff --git a/graphviz/reaction_to_catalyst_association.svg b/graphviz/reaction_to_catalyst_association.svg index bea2ccb638..848c987da8 100644 --- a/graphviz/reaction_to_catalyst_association.svg +++ b/graphviz/reaction_to_catalyst_association.svg @@ -4,16 +4,16 @@ - + %3 - + reaction to catalyst association - -reaction to catalyst association + +reaction to catalyst association @@ -24,9 +24,9 @@ reaction to catalyst association->reaction to participant association - - -is_a + + +is_a @@ -37,9 +37,9 @@ reaction to catalyst association->id - - -id + + +id @@ -50,9 +50,9 @@ reaction to catalyst association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ reaction to catalyst association->name - - -name + + +name @@ -76,9 +76,9 @@ reaction to catalyst association->description - - -description + + +description @@ -89,9 +89,9 @@ reaction to catalyst association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ reaction to catalyst association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ reaction to catalyst association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ reaction to catalyst association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ reaction to catalyst association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ reaction to catalyst association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ reaction to catalyst association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ reaction to catalyst association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ reaction to catalyst association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ reaction to catalyst association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ reaction to catalyst association->original subject - - -original subject + + +original subject @@ -232,9 +232,9 @@ reaction to catalyst association->original predicate - - -original predicate + + +original predicate @@ -245,149 +245,292 @@ reaction to catalyst association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +reaction to catalyst association->subject category + + +subject category + + + +object category + +ontology class + + + +reaction to catalyst association->object category + + +object category + + + +subject closure + +string + + + +reaction to catalyst association->subject closure + + +subject closure + + + +object closure + +string + + + +reaction to catalyst association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +reaction to catalyst association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +reaction to catalyst association->object category closure + + +object category closure + + + +subject namespace + +string + + + +reaction to catalyst association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +reaction to catalyst association->object namespace + + +object namespace + + + +subject label closure + +string + + + +reaction to catalyst association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +reaction to catalyst association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +reaction to catalyst association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + reaction to catalyst association->type - - -type + + +type - + category - -category + +category - + reaction to catalyst association->category - - -category + + +category - + stoichiometry - -integer + +integer - + reaction to catalyst association->stoichiometry - - -stoichiometry + + +stoichiometry - + reaction direction - -ReactionDirectionEnum + +ReactionDirectionEnum - + reaction to catalyst association->reaction direction - - -reaction direction + + +reaction direction - + reaction side - -ReactionSideEnum + +ReactionSideEnum - + reaction to catalyst association->reaction side - - -reaction side + + +reaction side - + subject - -subject + +subject - + reaction to catalyst association->subject - - -subject + + +subject - + object - -object + +object - + reaction to catalyst association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + reaction to participant association_subject - -molecular entity + +molecular entity - + object->relation - - + + - + reaction to catalyst association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/reaction_to_participant_association.gv b/graphviz/reaction_to_participant_association.gv index e2c27eb1ab..a719cc46fa 100644 --- a/graphviz/reaction_to_participant_association.gv +++ b/graphviz/reaction_to_participant_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3844.7,283"]; + graph [bb="0,0,5567.7,283"]; node [label="\N"]; "reaction to participant association" [height=0.5, label="reaction to participant association", - pos="2012.5,265", + pos="2905.5,265", width=4.7121]; "chemical to chemical association" [height=0.5, pos="162.49,178", width=4.5135]; "reaction to participant association" -> "chemical to chemical association" [label=is_a, - lp="482.49,221.5", - pos="e,236.63,194.09 1843.5,263.14 1500.1,260.91 730.8,253.28 468.49,229 392.96,222.01 307.87,207.57 246.63,195.99"]; + lp="481.49,221.5", + pos="e,235.75,194.14 2736.7,263.03 2221.7,259.85 691.36,248.85 467.49,229 391.92,222.3 306.8,207.75 245.72,196.07"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "reaction to participant association" -> id [color=blue, label=id, - lp="600.49,221.5", - pos="e,410.47,190.01 1843.4,263.51 1521.2,261.98 830.65,255.58 593.49,229 519.6,220.72 501.15,215.79 429.49,196 426.38,195.14 423.18,\ -194.18 419.98,193.17", + lp="598.49,221.5", + pos="e,410.47,190 2736.5,263.26 2239.2,260.82 802.31,251.87 591.49,229 518.44,221.08 500.29,215.65 429.49,196 426.38,195.14 423.18,194.17 \ +419.98,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "reaction to participant association" -> iri [color=blue, label=iri, - lp="719.49,221.5", - pos="e,515.1,190.17 1844.1,262.79 1543.4,260.07 925.84,251.83 711.49,229 632.35,220.57 612.64,215.53 535.49,196 532.06,195.13 528.52,\ -194.16 524.99,193.14", + lp="715.49,221.5", + pos="e,515.39,190.23 2736.5,263 2256.6,259.92 906.67,249.54 707.49,229 630.06,221.02 610.91,215.26 535.49,196 532.11,195.14 528.63,194.18 \ +525.14,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "reaction to participant association" -> name [color=blue, label=name, - lp="832.49,221.5", - pos="e,641.08,191.05 1843.8,263.13 1561.8,260.99 1006.6,253.69 812.49,229 756.3,221.86 693.29,205.84 650.87,193.85", + lp="826.49,221.5", + pos="e,640.29,191.28 2736.2,263.28 2271.1,261.01 995.15,252.68 806.49,229 752.09,222.17 691.23,206.24 650.06,194.18", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "reaction to participant association" -> description [color=blue, label=description, - lp="962.99,221.5", - pos="e,790.57,193.5 1843.1,263.77 1582.3,262.53 1094.5,256.46 922.49,229 880.37,222.28 834.01,208.29 800.2,196.82", + lp="953.99,221.5", + pos="e,788.74,193.79 2735.9,263.75 2287.2,262.71 1090.5,257.29 913.49,229 873.71,222.64 830.17,208.8 798.25,197.28", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "reaction to participant association" -> "has attribute" [color=blue, label="has attribute", - lp="1117.5,221.5", - pos="e,930.92,191.59 1844,262.64 1614.1,259.94 1214.4,252 1070.5,229 1025.4,221.8 975.52,206.69 940.75,194.95", + lp="1109.5,221.5", + pos="e,929.56,191.9 2736.4,263.42 2312.2,261.6 1224.8,254.48 1062.5,229 1019.6,222.27 972.44,207.28 939.35,195.45", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "reaction to participant association" -> predicate [color=blue, label=predicate, - lp="1272.5,221.5", - pos="e,1088.3,193.06 1847.8,260.55 1656.2,255.83 1351.6,245.95 1238.5,229 1190.3,221.79 1136.8,207.51 1098.2,196.05", + lp="1268.5,221.5", + pos="e,1086.9,193.25 2736.8,262.73 2342,259.43 1380.1,249.38 1234.5,229 1187,222.36 1134.5,207.95 1096.7,196.3", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "reaction to participant association" -> negated [color=blue, label=negated, - lp="1408.5,221.5", - pos="e,1221.7,190.33 1843.7,262.96 1715.7,260.17 1535.8,251.95 1379.5,229 1327.9,221.42 1270.1,205.31 1231.6,193.41", + lp="1410.5,221.5", + pos="e,1221.3,190.46 2735.6,264.59 2394.9,265.04 1638.6,262.1 1381.5,229 1328.9,222.23 1270.2,205.81 1231.3,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "reaction to participant association" -> qualifiers [color=blue, label=qualifiers, - lp="1539,221.5", - pos="e,1369.8,193.28 1846.5,261.16 1747,257.33 1618.3,248.61 1505.5,229 1462.2,221.48 1414.3,207.6 1379.3,196.37", + lp="1549,221.5", + pos="e,1370.2,193.2 2735.6,264.73 2418.1,265.25 1745.9,262.23 1515.5,229 1468.8,222.26 1417,207.87 1379.8,196.25", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "reaction to participant association" -> publications [color=blue, label=publications, - lp="1672.5,221.5", - pos="e,1518.9,193.32 1854.7,258.36 1784.8,253.62 1701.9,244.93 1628.5,229 1594,221.52 1556.4,208.14 1528.4,197.11", + lp="1694.5,221.5", + pos="e,1521.2,192.85 2735.8,264.85 2442.9,265.38 1854.1,262.09 1650.5,229 1609.1,222.28 1563.6,207.95 1530.9,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "reaction to participant association" -> "has evidence" [color=blue, label="has evidence", - lp="1812,221.5", - pos="e,1673.4,194.37 1889.8,252.57 1849.7,247.27 1805.3,239.69 1765.5,229 1737.1,221.39 1706.5,209.08 1682.8,198.58", + lp="1853,221.5", + pos="e,1679.5,193.63 2736,264.02 2473.4,263.13 1980.1,257.55 1806.5,229 1766.1,222.35 1721.7,208.52 1689.2,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "reaction to participant association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1941,221.5", - pos="e,1850.9,196.24 1919.5,249.88 1904.3,244.89 1889.3,238.13 1876.5,229 1867.9,222.9 1861,213.84 1855.7,205.1", + lp="2008,221.5", + pos="e,1869,195.61 2738.5,261.78 2483.3,257.8 2018,248.04 1943.5,229 1920.4,223.1 1896.4,211.34 1877.7,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "reaction to participant association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2108.5,221.5", - pos="e,2034.1,194.65 2008.7,246.59 2007.4,236.37 2007.6,223.63 2013.5,214 2016.7,208.82 2020.9,204.35 2025.7,200.52", + lp="2179.5,221.5", + pos="e,2075.5,196.33 2737.6,262.34 2504.4,259.25 2108,250.81 2084.5,229 2078.4,223.32 2076,214.91 2075.4,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "reaction to participant association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2333,221.5", - pos="e,2269.8,194.64 2123.4,251.34 2150.2,246.2 2178.4,239.02 2203.5,229 2214.8,224.48 2215.7,219.64 2226.5,214 2237.2,208.42 2249,203.13 \ -2260.4,198.44", + lp="2388,221.5", + pos="e,2291.7,195.87 2741.3,260.33 2561.8,255.49 2297.2,245.58 2281.5,229 2274.3,221.43 2277.8,212.05 2284.6,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "reaction to participant association" -> timepoint [color=blue, label=timepoint, - lp="2495.5,221.5", - pos="e,2479.5,195.4 2132.3,252.25 2152.1,250.42 2172.4,248.6 2191.5,247 2246.5,242.39 2388.6,250.55 2439.5,229 2446.9,225.85 2460.3,214.04 \ -2472.1,202.69", + lp="2542.5,221.5", + pos="e,2494.9,196.43 2746.3,258.74 2643.6,253.87 2525.9,244.88 2507.5,229 2500.9,223.36 2497.6,214.85 2496,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "reaction to participant association" -> "original subject" [color=blue, label="original subject", - lp="2610.5,221.5", - pos="e,2586.4,193.27 2130.9,252.05 2151.1,250.21 2171.9,248.45 2191.5,247 2267.2,241.41 2460.5,252.9 2532.5,229 2533.8,228.56 2557.5,\ -212.71 2577.9,198.98", + lp="2640.5,221.5", + pos="e,2591.7,194.82 2755.3,256.61 2677.7,251.21 2596.5,242.43 2584.5,229 2577.8,221.56 2580.4,211.86 2585.9,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,9 +170,8 @@ digraph { width=1.5887]; "reaction to participant association" -> "original predicate" [color=blue, label="original predicate", - lp="2751,221.5", - pos="e,2706.2,195.47 2129.4,251.93 2150.1,250.07 2171.4,248.33 2191.5,247 2244.3,243.5 2618.6,249.24 2667.5,229 2674.8,225.97 2687.7,\ -214.17 2699,202.79", + lp="2767,221.5", + pos="e,2707.7,195.8 2771.2,253.96 2740.3,248.77 2713.5,240.91 2703.5,229 2697.6,222.05 2698.9,213.06 2702.8,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -184,107 +180,224 @@ digraph { width=1.0652]; "reaction to participant association" -> "original object" [color=blue, label="original object", - lp="2881,221.5", - pos="e,2834.1,196.32 2128.9,251.82 2149.7,249.96 2171.2,248.25 2191.5,247 2226.2,244.85 2789.3,249.41 2817.5,229 2824.9,223.63 2829.3,\ -214.92 2831.8,206.26", + lp="2891,221.5", + pos="e,2832.9,196.07 2859.8,247.64 2851.9,242.81 2844.5,236.69 2839.5,229 2835.1,222.32 2833.3,214 2832.9,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2968.5,178", + width=2.1304]; + "reaction to participant association" -> "subject category" [color=blue, + label="subject category", + lp="3015,221.5", + pos="e,2963.1,196.22 2928.9,247.1 2935.2,241.81 2941.6,235.61 2946.5,229 2951.7,221.97 2956,213.49 2959.4,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3139.5,178", + width=2.1304]; + "reaction to participant association" -> "object category" [color=blue, + label="object category", + lp="3158,221.5", + pos="e,3123.4,195.91 3012,250.93 3034.6,245.84 3057.9,238.79 3078.5,229 3092.1,222.54 3105.3,212.41 3115.9,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3272.5,178", + width=1.0652]; + "reaction to participant association" -> "subject closure" [color=blue, + label="subject closure", + lp="3295,221.5", + pos="e,3259.4,195.42 3025.5,252.26 3109.6,243.76 3208.5,233.07 3217.5,229 3230.7,223.04 3242.8,212.72 3252.4,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3372.5,178", + width=1.0652]; + "reaction to participant association" -> "object closure" [color=blue, + label="object closure", + lp="3415.5,221.5", + pos="e,3370.7,196.22 3024.8,252.2 3044.7,250.36 3065.2,248.56 3084.5,247 3114.3,244.58 3329.4,246.82 3353.5,229 3360.9,223.52 3365.4,\ +214.78 3368.2,206.13", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3505.5,178", + width=2.1304]; + "reaction to participant association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3574,221.5", + pos="e,3498.1,196.1 3023.4,251.99 3043.7,250.15 3064.7,248.4 3084.5,247 3127.2,243.97 3431.8,249.41 3469.5,229 3479.5,223.59 3487.4,214.08 \ +3493.2,204.79", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3697.5,178", + width=2.1304]; + "reaction to participant association" -> "object category closure" [color=blue, + label="object category closure", + lp="3765,221.5", + pos="e,3691.5,196.11 3021.9,251.86 3042.7,250 3064.2,248.27 3084.5,247 3116.7,244.97 3637.4,244.94 3665.5,229 3674.9,223.66 3682,214.29 \ +3687,205.09", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3887.5,178", + width=1.0652]; + "reaction to participant association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3937.5,221.5", + pos="e,3880.5,196.18 3021.4,251.77 3042.4,249.91 3064.1,248.21 3084.5,247 3127.1,244.48 3814.9,249.15 3852.5,229 3862.3,223.75 3869.9,\ +214.39 3875.6,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4046.5,178", + width=1.0652]; + "reaction to participant association" -> "object namespace" [color=blue, + label="object namespace", + lp="4090.5,221.5", + pos="e,4039.1,195.73 3020.9,251.75 3042.1,249.87 3063.9,248.18 3084.5,247 3135.8,244.07 3963.8,252.58 4009.5,229 4019.8,223.67 4028,213.99 \ +4034,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4197.5,178", + width=1.0652]; + "reaction to participant association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4250.5,221.5", + pos="e,4189.5,195.76 3020.5,251.75 3041.7,249.86 3063.8,248.16 3084.5,247 3144.1,243.68 4105.1,255.63 4158.5,229 4169.2,223.66 4177.8,\ +213.84 4184.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4368.5,178", + width=1.0652]; + "reaction to participant association" -> "object label closure" [color=blue, + label="object label closure", + lp="4416,221.5", + pos="e,4360.2,195.79 3020.5,251.71 3041.7,249.82 3063.8,248.13 3084.5,247 3119,245.11 4297.4,244.2 4328.5,229 4339.3,223.69 4348.2,213.87 \ +4354.8,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4512.5,178", + width=2.347]; + "reaction to participant association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4572,221.5", + pos="e,4509.5,196.01 3020.5,251.68 3041.7,249.8 3063.8,248.12 3084.5,247 3123.5,244.9 4456.8,250.27 4489.5,229 4497.6,223.7 4502.9,214.72 \ +4506.4,205.82", style=solid]; type [height=0.5, - pos="2923.5,178", + pos="4646.5,178", width=0.86659]; "reaction to participant association" -> type [color=blue, label=type, - lp="2957.5,221.5", - pos="e,2934.5,194.96 2128.4,251.79 2149.4,249.92 2171.1,248.21 2191.5,247 2212.1,245.77 2922,243.81 2936.5,229 2942.9,222.4 2942.1,213.04 \ -2938.8,204.2", + lp="4668.5,221.5", + pos="e,4651.6,196.18 3020,251.7 3041.4,249.8 3063.6,248.11 3084.5,247 3106.1,245.85 4630.1,244.27 4645.5,229 4651.4,223.09 4653,214.51 \ +4652.7,206.12", style=solid]; category [height=0.5, - pos="3024.5,178", + pos="4747.5,178", width=1.4263]; "reaction to participant association" -> category [color=blue, label=category, - lp="3031,221.5", - pos="e,3014,195.81 2127.9,251.81 2149.1,249.93 2170.9,248.21 2191.5,247 2235.1,244.43 2937.6,246.79 2977.5,229 2989.6,223.62 3000,213.51 \ -3007.9,203.78", + lp="4746,221.5", + pos="e,4733.9,195.46 3020,251.69 3041.4,249.8 3063.6,248.11 3084.5,247 3129,244.64 4646.7,244.58 4688.5,229 4703.1,223.56 4716.5,212.8 \ +4726.9,202.65", style=solid]; object [height=0.5, - pos="3729.5,91", + pos="5452.5,91", width=1.0832]; "reaction to participant association" -> object [color=blue, label=object, - lp="3142.5,178", - pos="e,3690.4,92.466 2127.9,251.77 2149.1,249.89 2170.9,248.19 2191.5,247 2240,244.2 3023,250.74 3066.5,229 3101.3,211.58 3086.5,178.98 \ -3120.5,160 3216.3,106.55 3552.9,95.088 3680.2,92.651", + lp="4865.5,178", + pos="e,5413.6,92.765 3020,251.68 3041.4,249.79 3063.6,248.1 3084.5,247 3131.6,244.52 4738.5,248.42 4781.5,229 4819.1,212.01 4806.8,178.85 \ +4843.5,160 4941,109.84 5276.6,96.366 5403.4,93.024", style=solid]; stoichiometry [color=blue, height=0.5, label=integer, - pos="3217.5,178", + pos="4940.5,178", width=1.2277]; "reaction to participant association" -> stoichiometry [color=blue, label=stoichiometry, - lp="3213,221.5", - pos="e,3196.8,194.03 2127.9,251.75 2149.1,249.87 2170.9,248.17 2191.5,247 2295.1,241.09 3025.1,255.54 3125.5,229 3147.9,223.06 3170.9,\ -210.6 3188.2,199.61", + lp="4936,221.5", + pos="e,4919.8,194.09 3020,251.68 3041.4,249.78 3063.6,248.1 3084.5,247 3182.4,241.86 4753.6,253.63 4848.5,229 4871,223.16 4893.9,210.7 \ +4911.3,199.68", style=solid]; "reaction direction" [color=blue, height=0.5, label=ReactionDirectionEnum, - pos="3401.5,178", + pos="5124.5,178", width=3.3761]; "reaction to participant association" -> "reaction direction" [color=blue, label="reaction direction", - lp="3384,221.5", - pos="e,3367.2,195.4 2127.5,251.75 2148.7,249.86 2170.8,248.16 2191.5,247 2310.8,240.35 3149.1,251.06 3266.5,229 3298.1,223.06 3332,210.46 \ -3358,199.39", + lp="5107,221.5", + pos="e,5090.5,195.35 3020,251.66 3041.4,249.77 3063.6,248.09 3084.5,247 3190.2,241.49 4885.4,248.16 4989.5,229 5021.2,223.16 5055.3,210.48 \ +5081.3,199.36", style=solid]; "reaction side" [color=blue, height=0.5, label=ReactionSideEnum, - pos="3639.5,178", + pos="5362.5,178", width=2.7442]; "reaction to participant association" -> "reaction side" [color=blue, label="reaction side", - lp="3571,221.5", - pos="e,3594.9,194.18 2127.5,251.7 2148.7,249.82 2170.8,248.13 2191.5,247 2331.3,239.37 3312.8,248.14 3451.5,229 3497.4,222.66 3548.1,\ -208.75 3585.3,197.21", + lp="5294,221.5", + pos="e,5318.3,194.13 3020,251.65 3041.4,249.76 3063.6,248.08 3084.5,247 3316.4,235.01 4944.3,260.09 5174.5,229 5220.6,222.77 5271.5,208.78 \ +5308.7,197.18", style=solid]; subject [height=0.5, - pos="3800.5,178", + pos="5523.5,178", width=1.2277]; "reaction to participant association" -> subject [color=blue, label=subject, - lp="3716.5,221.5", - pos="e,3769,190.65 2127,251.72 2148.4,249.82 2170.6,248.12 2191.5,247 2350.2,238.48 3464,250.29 3621.5,229 3669.9,222.46 3723.6,206.19 \ -3759.4,193.97", + lp="5439.5,221.5", + pos="e,5492,190.69 3020,251.64 3041.4,249.75 3063.6,248.07 3084.5,247 3335.3,234.12 5095.6,262.07 5344.5,229 5392.9,222.57 5446.6,206.28 \ +5482.4,194.03", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2238.5,265", + pos="3131.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2369.5,265", + pos="3262.5,265", width=2.0762]; relation [height=0.5, - pos="3764.5,18", + pos="5487.5,18", width=1.2999]; - object -> relation [pos="e,3756,36.198 3737.8,73.174 3741.9,64.896 3746.9,54.723 3751.5,45.438", + object -> relation [pos="e,5479,36.198 5460.8,73.174 5464.9,64.896 5469.9,54.723 5474.5,45.438", style=dotted]; "chemical to chemical association_object" [color=blue, height=0.5, label="chemical entity", - pos="2544.5,265", + pos="3437.5,265", width=2.2748]; subject -> object [label=relation, - lp="3758.5,134.5", - pos="e,3725.7,109.01 3764.1,167.42 3751.3,162.12 3738.1,154.06 3730.5,142 3726.2,135.26 3724.9,126.93 3724.9,119.01"]; - subject -> relation [pos="e,3768.7,36.005 3796.8,160.05 3792.4,139.44 3784.6,103.63 3777.5,73 3775.4,64.183 3773.2,54.574 3771.1,45.938", + lp="5481.5,134.5", + pos="e,5448.7,109.01 5487.1,167.42 5474.3,162.12 5461.1,154.06 5453.5,142 5449.2,135.26 5447.9,126.93 5447.9,119.01"]; + subject -> relation [pos="e,5491.7,36.005 5519.8,160.05 5515.4,139.44 5507.6,103.63 5500.5,73 5498.4,64.183 5496.2,54.574 5494.1,45.938", style=dotted]; "reaction to participant association_subject" [color=blue, height=0.5, label="molecular entity", - pos="2731.5,265", + pos="3624.5,265", width=2.4192]; } diff --git a/graphviz/reaction_to_participant_association.svg b/graphviz/reaction_to_participant_association.svg index 9794d0eeb9..eb33d0efc8 100644 --- a/graphviz/reaction_to_participant_association.svg +++ b/graphviz/reaction_to_participant_association.svg @@ -4,16 +4,16 @@ - + %3 - + reaction to participant association - -reaction to participant association + +reaction to participant association @@ -24,9 +24,9 @@ reaction to participant association->chemical to chemical association - - -is_a + + +is_a @@ -37,9 +37,9 @@ reaction to participant association->id - - -id + + +id @@ -50,9 +50,9 @@ reaction to participant association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ reaction to participant association->name - - -name + + +name @@ -76,9 +76,9 @@ reaction to participant association->description - - -description + + +description @@ -89,9 +89,9 @@ reaction to participant association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ reaction to participant association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ reaction to participant association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ reaction to participant association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ reaction to participant association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ reaction to participant association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ reaction to participant association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ reaction to participant association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ reaction to participant association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ reaction to participant association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ reaction to participant association->original subject - - -original subject + + +original subject @@ -232,9 +232,9 @@ reaction to participant association->original predicate - - -original predicate + + +original predicate @@ -245,149 +245,292 @@ reaction to participant association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +reaction to participant association->subject category + + +subject category + + + +object category + +ontology class + + + +reaction to participant association->object category + + +object category + + + +subject closure + +string + + + +reaction to participant association->subject closure + + +subject closure + + + +object closure + +string + + + +reaction to participant association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +reaction to participant association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +reaction to participant association->object category closure + + +object category closure + + + +subject namespace + +string + + + +reaction to participant association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +reaction to participant association->object namespace + + +object namespace + + + +subject label closure + +string + + + +reaction to participant association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +reaction to participant association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +reaction to participant association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + reaction to participant association->type - - -type + + +type - + category - -category + +category - + reaction to participant association->category - - -category + + +category - + object - -object + +object - + reaction to participant association->object - - -object + + +object - + stoichiometry - -integer + +integer - + reaction to participant association->stoichiometry - - -stoichiometry + + +stoichiometry - + reaction direction - -ReactionDirectionEnum + +ReactionDirectionEnum - + reaction to participant association->reaction direction - - -reaction direction + + +reaction direction - + reaction side - -ReactionSideEnum + +ReactionSideEnum - + reaction to participant association->reaction side - - -reaction side + + +reaction side - + subject - -subject + +subject - + reaction to participant association->subject - - -subject + + +subject - + association_type - -string + +string - + association_category - -category type + +category type - + relation - -relation + +relation - + object->relation - - + + - + chemical to chemical association_object - -chemical entity + +chemical entity - + subject->object - - -relation + + +relation - + subject->relation - - + + - + reaction to participant association_subject - -molecular entity + +molecular entity diff --git a/graphviz/retrieval_source.gv b/graphviz/retrieval_source.gv index 8b04159256..bdb8f7a0e4 100644 --- a/graphviz/retrieval_source.gv +++ b/graphviz/retrieval_source.gv @@ -1,5 +1,5 @@ digraph { - graph [bb="0,0,2206.4,123"]; + graph [bb="0,0,2252.4,123"]; node [label="\N"]; "retrieval source" [height=0.5, label="retrieval source", @@ -133,50 +133,50 @@ digraph { pos="e,1516.3,32.63 1213.1,92.226 1224.1,90.302 1235.5,88.463 1246.2,87 1334.2,75.003 1360.4,95.129 1445.2,69 1467.6,62.103 1490.7,49.151 \ 1507.9,38.158", style=solid]; - resource [height=0.5, - pos="1636.2,18", - width=1.4263]; - "retrieval source" -> resource [color=blue, - label=resource, - lp="1633.7,61.5", - pos="e,1622.4,35.72 1212.1,92.078 1223.4,90.121 1235.2,88.308 1246.2,87 1319.6,78.34 1509.7,96.599 1578.2,69 1592.2,63.381 1605.1,52.96 \ -1615.3,43.081", + "resource id" [height=0.5, + pos="1647.2,18", + width=1.7512]; + "retrieval source" -> "resource id" [color=blue, + label="resource id", + lp="1645.7,61.5", + pos="e,1630.4,35.495 1212.1,92.078 1223.4,90.121 1235.2,88.308 1246.2,87 1319.6,78.34 1508.6,93.683 1578.2,69 1594.6,63.203 1610.4,52.22 \ +1622.8,42.021", style=solid]; "resource role" [height=0.5, - pos="1777.2,18", + pos="1800.2,18", width=2.004]; "retrieval source" -> "resource role" [color=blue, label="resource role", - lp="1760.7,61.5", - pos="e,1750.8,34.821 1212.1,91.973 1223.4,90.026 1235.1,88.244 1246.2,87 1339.7,76.516 1577.8,91.186 1669.2,69 1694.7,62.831 1721.4,50.534 \ -1741.8,39.68", - style=solid]; - "upstream resources" [height=0.5, - pos="1970.2,18", - width=2.8706]; - "retrieval source" -> "upstream resources" [color=blue, - label="upstream resources", - lp="1945.7,61.5", - pos="e,1931.1,34.723 1211.6,91.963 1223,89.99 1235,88.202 1246.2,87 1496.5,60.298 1564.1,111.37 1812.2,69 1849.7,62.598 1890.6,49.475 \ -1921.4,38.28", + lp="1781.7,61.5", + pos="e,1773.3,34.835 1212.1,91.955 1223.4,90.01 1235.1,88.233 1246.2,87 1344.4,76.095 1594.2,91.856 1690.2,69 1716.2,62.825 1743.5,50.445 \ +1764.4,39.55", + style=solid]; + "upstream resource ids" [height=0.5, + pos="2005.2,18", + width=3.1955]; + "retrieval source" -> "upstream resource ids" [color=blue, + label="upstream resource ids", + lp="1981.7,61.5", + pos="e,1962.5,34.714 1211.6,91.952 1223,89.981 1235,88.195 1246.2,87 1505.8,59.455 1575.4,109.75 1833.2,69 1874.2,62.526 1919.1,49.232 \ +1952.8,37.978", style=solid]; xref [color=blue, height=0.5, label=uriorcurie, - pos="2149.2,18", + pos="2195.2,18", width=1.5887]; "retrieval source" -> xref [color=blue, label=xref, - lp="2085.7,61.5", - pos="e,2120.4,33.642 1211.6,91.885 1223,89.92 1235,88.153 1246.2,87 1417.6,69.457 1852.3,102.85 2021.2,69 2052.7,62.702 2086.4,49.245 \ -2111.3,37.877", + lp="2130.7,61.5", + pos="e,2166.1,33.653 1211.6,91.874 1223,89.909 1235,88.146 1246.2,87 1427.6,68.555 1887.5,104.47 2066.2,69 2097.9,62.721 2131.8,49.263 \ +2157,37.89", style=solid]; "named thing_category" [color=blue, height=0.5, label="category type", pos="1330.2,105", width=2.0762]; - "retrieval source_resource" [color=blue, + "retrieval source_resource id" [color=blue, height=0.5, label=uriorcurie, pos="1480.2,105", @@ -186,7 +186,7 @@ digraph { label=ResourceRoleEnum, pos="1657.2,105", width=2.8164]; - "retrieval source_upstream resources" [color=blue, + "retrieval source_upstream resource ids" [color=blue, height=0.5, label=uriorcurie, pos="1834.2,105", diff --git a/graphviz/retrieval_source.svg b/graphviz/retrieval_source.svg index bfe8ad9439..9629db7d5e 100644 --- a/graphviz/retrieval_source.svg +++ b/graphviz/retrieval_source.svg @@ -4,11 +4,11 @@ - + %3 - + retrieval source @@ -184,57 +184,57 @@ creation date - + -resource - -resource +resource id + +resource id - + -retrieval source->resource - - -resource +retrieval source->resource id + + +resource id resource role - -resource role + +resource role retrieval source->resource role - - -resource role + + +resource role - + -upstream resources - -upstream resources +upstream resource ids + +upstream resource ids - + -retrieval source->upstream resources - - -upstream resources +retrieval source->upstream resource ids + + +upstream resource ids xref - -uriorcurie + +uriorcurie retrieval source->xref - - -xref + + +xref @@ -242,9 +242,9 @@ category type - + -retrieval source_resource +retrieval source_resource id uriorcurie @@ -254,9 +254,9 @@ ResourceRoleEnum - + -retrieval source_upstream resources +retrieval source_upstream resource ids uriorcurie diff --git a/graphviz/sequence_association.gv b/graphviz/sequence_association.gv index eb215ec846..d8b505875f 100644 --- a/graphviz/sequence_association.gv +++ b/graphviz/sequence_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3188.7,283"]; + graph [bb="0,0,4878.7,283"]; node [label="\N"]; "sequence association" [height=0.5, label="sequence association", - pos="1444.4,265", + pos="2498.4,265", width=3.015]; association [height=0.5, pos="62.394,178", width=1.7332]; "sequence association" -> association [label=is_a, - lp="282.39,221.5", - pos="e,103.34,191.62 1335.9,263.66 1085.3,262.4 472.59,256.51 268.39,229 214.65,221.76 154.53,206.29 113.17,194.46"]; + lp="280.39,221.5", + pos="e,102.91,191.79 2389.9,263.73 1971.7,262.49 477.62,256.19 266.39,229 213.1,222.14 153.57,206.61 112.64,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "sequence association" -> id [color=blue, label=id, - lp="400.39,221.5", - pos="e,210.37,190.01 1336.4,262.67 1106.1,259.46 573.38,249.96 393.39,229 319.54,220.4 301.06,215.79 229.39,196 226.28,195.14 223.08,\ -194.18 219.89,193.17", + lp="396.39,221.5", + pos="e,210.38,189.98 2390.1,263.39 1987.2,260.95 588.45,250.98 389.39,229 317.23,221.03 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "sequence association" -> iri [color=blue, label=iri, - lp="513.39,221.5", - pos="e,315.3,190.22 1337.2,262.09 1126.1,257.98 663.51,247.18 505.39,229 428.93,220.21 409.95,215.12 335.39,196 332.02,195.13 328.54,\ -194.17 325.05,193.16", + lp="503.39,221.5", + pos="e,315.31,190.16 2390.2,263.29 2000.8,260.56 683.57,249.87 495.39,229 423.23,221 405.62,214.45 335.39,196 332.02,195.11 328.55,194.14 \ +325.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "sequence association" -> name [color=blue, label=name, - lp="615.39,221.5", - pos="e,439.55,191.39 1336.9,262.39 1141.4,259 735.22,249.66 595.39,229 544.86,221.53 488.45,206.17 449.55,194.44", + lp="607.39,221.5", + pos="e,438.25,191.77 2390,263.56 2011.9,261.81 765.43,254.17 587.39,229 538.92,222.15 485.05,206.78 447.81,194.87", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "sequence association" -> description [color=blue, label=description, - lp="729.89,221.5", - pos="e,584.61,194.25 1336.4,262.98 1158,260.64 809.87,253.04 689.39,229 656.45,222.43 620.85,209.37 594.06,198.24", + lp="723.89,221.5", + pos="e,582.77,194.4 2390,264.07 2024.3,263.99 850.26,261.21 683.39,229 651.71,222.88 617.7,209.83 592.13,198.6", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "sequence association" -> "has attribute" [color=blue, label="has attribute", - lp="866.39,221.5", - pos="e,724.36,193.48 1337.1,262.25 1185,259.03 914.82,250.44 819.39,229 789.41,222.26 757.3,208.99 733.41,197.8", + lp="862.39,221.5", + pos="e,722.86,193.55 2389.7,264.11 2041.6,264.12 968.34,261.48 815.39,229 786.11,222.78 754.98,209.44 731.91,198.1", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { "sequence association" -> subject [color=blue, label=subject, lp="989.39,221.5", - pos="e,867.13,194.15 1339.9,260.09 1220.5,254.96 1032.5,244.73 963.39,229 933.31,222.15 900.97,209.33 876.46,198.39", + pos="e,866.52,194.37 2389.9,263.73 2063.1,262.6 1101.8,256.91 963.39,229 932.94,222.86 900.37,209.9 875.84,198.71", style=solid]; predicate [color=blue, height=0.5, @@ -81,7 +81,7 @@ digraph { "sequence association" -> predicate [color=blue, label=predicate, lp="1068.4,221.5", - pos="e,1008.8,196.39 1340.2,259.88 1227.4,254.66 1060,244.45 1034.4,229 1025.4,223.54 1018.4,214.45 1013.4,205.5", + pos="e,1008.4,196.14 2389.9,264.18 2060.9,264.37 1093.2,262.09 1034.4,229 1025,223.69 1017.9,214.33 1012.8,205.13", style=solid]; object [color=blue, height=0.5, @@ -91,8 +91,8 @@ digraph { "sequence association" -> object [color=blue, label=object, lp="1147.4,178", - pos="e,976.03,105.47 1345.5,257.55 1279.8,249.85 1193.4,232.97 1125.4,196 1105.5,185.2 1108.1,172.77 1089.4,160 1057.3,138.07 1017,120.64 \ -985.5,108.92", + pos="e,976.03,105.47 2390.9,262.4 2144.4,258.48 1543.9,247.3 1342.4,229 1245.2,220.17 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,172.77 \ +1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", style=solid]; negated [color=blue, height=0.5, @@ -101,8 +101,8 @@ digraph { width=1.2999]; "sequence association" -> negated [color=blue, label=negated, - lp="1368.4,221.5", - pos="e,1254.1,192.48 1396,248.89 1378.1,243.03 1357.7,236.04 1339.4,229 1313.7,219.12 1285.4,206.72 1263.5,196.74", + lp="1452.4,221.5", + pos="e,1260,190.37 2390.1,263.14 2155.7,260.86 1607.7,253.04 1423.4,229 1369.6,221.98 1309.4,205.49 1269.6,193.36", style=solid]; qualifiers [color=blue, height=0.5, @@ -111,8 +111,8 @@ digraph { width=2.1304]; "sequence association" -> qualifiers [color=blue, label=qualifiers, - lp="1443.9,221.5", - pos="e,1381.9,195.89 1428.6,246.8 1417.2,234.39 1401.7,217.46 1389,203.62", + lp="1585.9,221.5", + pos="e,1408.3,193.18 2390.3,263.06 2177.4,260.71 1710.9,252.93 1552.4,229 1506.1,222.01 1454.8,207.72 1417.8,196.19", style=solid]; publications [color=blue, height=0.5, @@ -121,8 +121,8 @@ digraph { width=1.7332]; "sequence association" -> publications [color=blue, label=publications, - lp="1539.4,221.5", - pos="e,1510.2,195.62 1463.2,246.96 1469.2,241.37 1475.7,235.05 1481.4,229 1489,220.96 1496.9,211.79 1503.8,203.52", + lp="1723.4,221.5", + pos="e,1558,193.06 2390.4,262.96 2200.2,260.54 1812.7,252.76 1679.4,229 1640.7,222.11 1598.4,208.11 1567.6,196.67", style=solid]; "has evidence" [color=blue, height=0.5, @@ -131,8 +131,8 @@ digraph { width=2.0943]; "sequence association" -> "has evidence" [color=blue, label="has evidence", - lp="1665.9,221.5", - pos="e,1654.1,195.08 1513.1,250.95 1537.1,245.43 1563.8,238.12 1587.4,229 1607.3,221.31 1628.3,210.17 1645.1,200.36", + lp="1869.9,221.5", + pos="e,1713.8,194.06 2391.1,262.12 2228.8,258.64 1928.8,249.61 1823.4,229 1788.9,222.26 1751.4,209.05 1723.4,197.9", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -141,9 +141,8 @@ digraph { width=3.015]; "sequence association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1836.9,221.5", - pos="e,1837.8,194.53 1522.4,252.46 1535.8,250.57 1549.5,248.69 1562.4,247 1630.7,238.09 1648.9,243.05 1716.4,229 1754.4,221.09 1796.2,\ -208.38 1828.2,197.75", + lp="2009.9,221.5", + pos="e,1897.3,195.93 2389.8,264.68 2252.3,264.25 2023.9,258.82 1945.4,229 1930.4,223.32 1916.2,212.85 1904.9,202.96", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -152,9 +151,8 @@ digraph { width=3.015]; "sequence association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2077.4,221.5", - pos="e,2064.9,193.96 1520.1,252.05 1534.2,250.14 1548.7,248.34 1562.4,247 1714.3,232.1 1754.3,250.69 1905.4,229 1956.5,221.67 2013.3,\ -207.87 2055.1,196.61", + lp="2176.4,221.5", + pos="e,2093.1,195.58 2391,262.38 2274.4,259.48 2102,251.41 2081.4,229 2074.1,221.04 2078.2,211.47 2085.7,202.85", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -163,9 +161,8 @@ digraph { width=3.015]; "sequence association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2351.9,221.5", - pos="e,2308.2,194.6 1519.2,251.92 1533.5,249.98 1548.4,248.21 1562.4,247 1698.4,235.25 2041.5,249.91 2176.4,229 2218.2,222.52 2264.1,\ -209.16 2298.4,197.88", + lp="2385.9,221.5", + pos="e,2303,194.15 2394,259.99 2345.3,255.69 2294.7,246.91 2279.4,229 2269.3,217.19 2278.7,206.86 2293.6,198.69", style=solid]; timepoint [color=blue, height=0.5, @@ -174,9 +171,8 @@ digraph { width=1.5346]; "sequence association" -> timepoint [color=blue, label=timepoint, - lp="2527.4,221.5", - pos="e,2516.6,195.21 1518.8,251.86 1533.2,249.91 1548.3,248.15 1562.4,247 1662.1,238.85 2367.4,260.16 2462.4,229 2479.4,223.41 2496,212.22 \ -2508.8,201.85", + lp="2534.4,221.5", + pos="e,2513.1,194.83 2495.7,246.69 2494.9,236.76 2495.1,224.26 2499.4,214 2501.1,209.95 2503.5,206.11 2506.2,202.56", style=solid]; "original subject" [color=blue, height=0.5, @@ -185,49 +181,168 @@ digraph { width=1.0652]; "sequence association" -> "original subject" [color=blue, label="original subject", - lp="2655.4,221.5", - pos="e,2627.7,194.27 1518.8,251.84 1533.2,249.89 1548.3,248.14 1562.4,247 1673.6,238.03 2459.5,261.02 2566.4,229 2585.8,223.2 2605,211.21 \ -2619.6,200.42", + lp="2647.4,221.5", + pos="e,2623.9,193.16 2533.2,247.93 2544.8,242.25 2557.8,235.62 2569.4,229 2570.6,228.29 2594.6,212.48 2615.4,198.82", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2760.4,178", + pos="2759.4,178", width=1.5887]; "sequence association" -> "original predicate" [color=blue, label="original predicate", - lp="2799.9,221.5", - pos="e,2750.6,195.83 1518.8,251.81 1533.2,249.86 1548.3,248.12 1562.4,247 1626.3,241.92 2657.1,255.52 2715.4,229 2727.1,223.69 2737,213.73 \ -2744.6,204.09", + lp="2789.9,221.5", + pos="e,2745.8,195.62 2578,252.67 2630.9,244.75 2692.8,234.63 2704.4,229 2717.2,222.76 2729.2,212.6 2738.7,203.05", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2910.4,178", + pos="2873.4,178", width=1.0652]; "sequence association" -> "original object" [color=blue, label="original object", - lp="2938.9,221.5", - pos="e,2901.2,195.82 1518.5,251.83 1533,249.87 1548.2,248.12 1562.4,247 1598.5,244.16 2834.6,244.35 2867.4,229 2878.8,223.68 2888.3,213.72 \ -2895.5,204.08", + lp="2917.9,221.5", + pos="e,2871.5,196.19 2575.1,252.18 2588.8,250.29 2603,248.47 2616.4,247 2642.8,244.11 2833.1,244.87 2854.4,229 2861.8,223.49 2866.3,214.74 \ +2869,206.09", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3006.4,178", + width=2.1304]; + "sequence association" -> "subject category" [color=blue, + label="subject category", + lp="3048.9,221.5", + pos="e,3000,196.05 2574.1,252.03 2588.2,250.12 2602.7,248.33 2616.4,247 2655.9,243.16 2938.9,248.7 2973.4,229 2982.9,223.58 2990.1,214.2 \ +2995.4,205.01", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3177.4,178", + width=2.1304]; + "sequence association" -> "object category" [color=blue, + label="object category", + lp="3195.9,221.5", + pos="e,3161.5,195.84 2573.5,251.96 2587.7,250.02 2602.5,248.25 2616.4,247 2671.3,242.06 3060.5,247.7 3112.4,229 3127.8,223.43 3142.6,\ +212.72 3154.1,202.64", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3310.4,178", + width=1.0652]; + "sequence association" -> "subject closure" [color=blue, + label="subject closure", + lp="3333.9,221.5", + pos="e,3297.9,195.35 2573.2,251.91 2587.5,249.97 2602.4,248.2 2616.4,247 2687.2,240.93 3189.5,255.54 3255.4,229 3269.1,223.47 3281.6,\ +212.85 3291.2,202.81", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3408.4,178", + width=1.0652]; + "sequence association" -> "object closure" [color=blue, + label="object closure", + lp="3450.4,221.5", + pos="e,3406.3,196.39 2572.8,251.9 2587.2,249.94 2602.3,248.18 2616.4,247 2659.1,243.43 3353.2,253.46 3388.4,229 3396.1,223.65 3400.8,\ +214.83 3403.7,206.06", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3541.4,178", + width=2.1304]; + "sequence association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3608.9,221.5", + pos="e,3533.8,196.22 2572.8,251.86 2587.2,249.91 2602.3,248.16 2616.4,247 2665.6,242.97 3460.6,251.65 3504.4,229 3514.6,223.74 3522.7,\ +214.25 3528.7,204.94", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3731.4,178", + width=2.1304]; + "sequence association" -> "object category closure" [color=blue, + label="object category closure", + lp="3798.9,221.5", + pos="e,3725.7,196.15 2572.8,251.82 2587.2,249.87 2602.3,248.13 2616.4,247 2646.4,244.6 3674.2,243.86 3700.4,229 3709.6,223.76 3716.5,\ +214.54 3721.3,205.43", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3921.4,178", + width=1.0652]; + "sequence association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3971.4,221.5", + pos="e,3914.7,195.72 2572.5,251.83 2587,249.87 2602.2,248.12 2616.4,247 2651.6,244.23 3855.2,245.51 3886.4,229 3896.5,223.66 3904.3,213.98 \ +3909.9,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4080.4,178", + width=1.0652]; + "sequence association" -> "object namespace" [color=blue, + label="object namespace", + lp="4124.4,221.5", + pos="e,4073,195.76 2572.5,251.82 2587,249.86 2602.2,248.11 2616.4,247 2655.9,243.92 4008.1,247.07 4043.4,229 4053.7,223.7 4061.9,214.03 \ +4067.9,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4231.4,178", + width=1.0652]; + "sequence association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4284.4,221.5", + pos="e,4223.4,195.79 2572.5,251.8 2587,249.85 2602.2,248.1 2616.4,247 2660,243.62 4153.2,248.43 4192.4,229 4203.1,223.69 4211.8,213.87 \ +4218.2,204.33", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4402.4,178", + width=1.0652]; + "sequence association" -> "object label closure" [color=blue, + label="object label closure", + lp="4450.9,221.5", + pos="e,4394.1,195.8 2572.5,251.79 2587,249.83 2602.2,248.09 2616.4,247 2664.8,243.28 4318.8,250.24 4362.4,229 4373.3,223.71 4382.1,213.89 \ +4388.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4564.4,178", + width=2.347]; + "sequence association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4612.9,221.5", + pos="e,4555.8,196.3 2572.5,251.78 2587,249.82 2602.2,248.09 2616.4,247 2669.2,242.96 4476.7,252.19 4524.4,229 4535.1,223.79 4543.9,214.17 \ +4550.4,204.76", style=solid]; type [height=0.5, - pos="3036.4,178", + pos="4726.4,178", width=0.86659]; "sequence association" -> type [color=blue, label=type, - lp="3030.4,221.5", - pos="e,3027.8,195.32 1518.5,251.82 1533,249.86 1548.2,248.11 1562.4,247 1602.1,243.91 2958.4,246.03 2994.4,229 3005.8,223.6 3015.2,213.43 \ -3022.3,203.67", + lp="4721.4,221.5", + pos="e,4718.1,195.81 2572.5,251.77 2587,249.82 2602.2,248.08 2616.4,247 2673.7,242.64 4634.7,254.13 4686.4,229 4697.3,223.72 4706.1,213.9 \ +4712.7,204.36", style=solid]; category [height=0.5, - pos="3137.4,178", + pos="4827.4,178", width=1.4263]; "sequence association" -> category [color=blue, label=category, - lp="3116.9,221.5", - pos="e,3116.9,194.8 1518.5,251.81 1533,249.85 1548.2,248.11 1562.4,247 1644.8,240.59 2970.6,250.8 3050.4,229 3071.2,223.3 3092.3,211.39 \ -3108.5,200.62", + lp="4807.9,221.5", + pos="e,4807.2,194.82 2572.5,251.77 2587,249.81 2602.2,248.08 2616.4,247 2734.1,238.06 4627.5,260.21 4741.4,229 4762.1,223.34 4782.9,211.42 \ +4798.9,200.65", style=solid]; subject -> object [label=relation, lp="919.39,134.5", @@ -242,11 +357,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="1609.4,265", + pos="2663.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1740.4,265", + pos="2794.4,265", width=2.0762]; } diff --git a/graphviz/sequence_association.svg b/graphviz/sequence_association.svg index 309ee3f7f7..e80f62661b 100644 --- a/graphviz/sequence_association.svg +++ b/graphviz/sequence_association.svg @@ -4,16 +4,16 @@ - + %3 - + sequence association - -sequence association + +sequence association @@ -24,9 +24,9 @@ sequence association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ sequence association->id - - -id + + +id @@ -50,9 +50,9 @@ sequence association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ sequence association->name - - -name + + +name @@ -76,9 +76,9 @@ sequence association->description - - -description + + +description @@ -89,9 +89,9 @@ sequence association->has attribute - - -has attribute + + +has attribute @@ -102,8 +102,8 @@ sequence association->subject - - + + subject @@ -115,8 +115,8 @@ sequence association->predicate - - + + predicate @@ -128,7 +128,7 @@ sequence association->object - + object @@ -141,9 +141,9 @@ sequence association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ sequence association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ sequence association->publications - - -publications + + +publications @@ -180,9 +180,9 @@ sequence association->has evidence - - -has evidence + + +has evidence @@ -193,9 +193,9 @@ sequence association->knowledge source - - -knowledge source + + +knowledge source @@ -206,9 +206,9 @@ sequence association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -219,9 +219,9 @@ sequence association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -232,9 +232,9 @@ sequence association->timepoint - - -timepoint + + +timepoint @@ -245,98 +245,241 @@ sequence association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie sequence association->original predicate - - -original predicate + + +original predicate original object - -string + +string sequence association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +sequence association->subject category + + +subject category + + + +object category + +ontology class + + + +sequence association->object category + + +object category + + + +subject closure + +string + + + +sequence association->subject closure + + +subject closure + + + +object closure + +string + + + +sequence association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +sequence association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +sequence association->object category closure + + +object category closure + + + +subject namespace + +string + + + +sequence association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +sequence association->object namespace + + +object namespace + + + +subject label closure + +string + + + +sequence association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +sequence association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +sequence association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + sequence association->type - - -type + + +type - + category - -category + +category - + sequence association->category - - -category + + +category - + subject->object relation - + relation relation - + subject->relation - + object->relation - + association_type - -string + +string - + association_category - -category type + +category type diff --git a/graphviz/sequence_feature_relationship.gv b/graphviz/sequence_feature_relationship.gv index 18a05aaf1d..a6f73fa988 100644 --- a/graphviz/sequence_feature_relationship.gv +++ b/graphviz/sequence_feature_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "sequence feature relationship" [height=0.5, label="sequence feature relationship", - pos="1542.4,265", + pos="2492.4,265", width=4.1524]; association [height=0.5, pos="62.394,178", width=1.7332]; "sequence feature relationship" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1393.1,263.82 1105,262.81 482.25,257.32 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2343.2,263.59 1877.9,262.02 471.57,255.17 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "sequence feature relationship" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1394.3,262.51 1129.5,259.34 585.16,250.39 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,\ -194.16 219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2343.4,263.11 1896,260.2 583.43,249.98 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "sequence feature relationship" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1395.5,261.57 1154.3,257.14 684.62,246.55 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,\ -194.19 324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2343.7,262.85 1913.6,259.33 687.81,247.76 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ +194.18 325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "sequence feature relationship" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1395.1,261.66 1172.8,257.59 762.4,247.77 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2343.8,263.06 1928.8,260.18 777.28,250.35 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "sequence feature relationship" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1394.7,262.01 1194.2,258.57 846.57,249.76 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2343.3,263.42 1944.7,261.54 873.62,254.18 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "sequence feature relationship" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1397.8,260.4 1230.8,255.55 966.45,245.57 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2343.6,263.04 1969.5,260.31 1009.7,251.21 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "sequence feature relationship" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1396.2,261.22 1294.2,257.51 1155.3,248.89 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2342.8,264.67 2024.3,265.39 1288.2,263.15 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "sequence feature relationship" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1410.3,256.47 1339.4,251.18 1250.8,242.57 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2343.2,263.57 2050.5,262.13 1410,255.9 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "sequence feature relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1431.5,252.9 1386.5,247.33 1334.2,239.48 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2343.3,263.64 2073.8,262.29 1515.8,256.2 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "sequence feature relationship" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1467.8,249.39 1444.1,243.93 1417.9,237.07 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2343.2,263.59 2098.4,262.13 1621.7,255.82 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "sequence feature relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461.1,195.6 1522,246.8 1506.7,233.96 1485.7,216.27 1468.9,202.19", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2343.7,262.7 2129.3,260.04 1743.7,252.12 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "sequence feature relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.2,247.31 1578.6,241.84 1587.6,235.49 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2342.5,264.73 2155.9,264.3 1848.2,258.84 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "sequence feature relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1638.2,251.13 1672.1,245.6 1710.2,238.25 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2346.9,260.69 2170.1,255.94 1893.3,245.86 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "sequence feature relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.8,195.18 1647.5,252.12 1665.5,250.27 1684,248.49 1701.4,247 1826.5,236.32 1860.7,255.85 1983.4,229 2013.5,222.42 2045.7,210.03 \ -2070.6,199.23", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2346,261.3 2233,257.65 2092.9,249.08 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "sequence feature relationship" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.77 1645.4,251.87 1664,250 1683.3,248.27 1701.4,247 1762.1,242.76 2193,254.05 2248.4,229 2260.4,223.56 2270.9,213.44 \ -2278.8,203.72", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2370.8,254.5 2337.7,249.32 2308.1,241.32 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "sequence feature relationship" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.22 1644.9,251.84 1663.7,249.96 1683.1,248.23 1701.4,247 1772.5,242.21 2275.3,252.89 2342.4,229 2351.2,225.86 2368.2,\ -212.73 2382.5,200.71", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2401.4,250.57 2390.9,245.4 2381.4,238.42 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,203 @@ digraph { width=1.5887]; "sequence feature relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.24 1644.5,251.81 1663.4,249.92 1683,248.2 1701.4,247 1744.6,244.19 2442.5,248.23 2481.4,229 2492.1,223.71 2500.8,214.09 \ -2507.4,204.69", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "sequence feature relationship" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.98 1644.1,251.8 1663.1,249.89 1682.8,248.17 1701.4,247 1727.2,245.38 2608.8,243.13 2630.4,229 2638.5,223.68 2643.8,\ -214.69 2647.3,205.79", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2585.2,250.84 2598.2,245.7 2610.5,238.65 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "sequence feature relationship" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2601.8,252.66 2661.5,245.72 2725.6,236.71 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "sequence feature relationship" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.5,195.83 2598.4,252.27 2616.1,250.43 2634.3,248.6 2651.4,247 2701.1,242.35 2828.9,247.14 2875.4,229 2890.3,223.19 2904.6,\ +212.71 2915.8,202.84", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "sequence feature relationship" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.25 2596.2,252.03 2614.6,250.16 2633.5,248.39 2651.4,247 2691.9,243.84 2978.8,244.4 3016.4,229 3030.2,223.33 3042.9,\ +212.69 3052.7,202.69", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "sequence feature relationship" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.34 2595.4,251.92 2614,250.04 2633.3,248.29 2651.4,247 2679.2,245.02 3129.6,245.03 3152.4,229 3160.1,223.61 3164.8,214.77 \ +3167.7,206.01", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "sequence feature relationship" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.18 2594.9,251.86 2613.7,249.97 2633.1,248.24 2651.4,247 2685.6,244.68 3238,244.88 3268.4,229 3278.5,223.69 3286.6,214.2 \ +3292.6,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "sequence feature relationship" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.16 2594.5,251.8 2613.4,249.9 2633,248.19 2651.4,247 2696.5,244.1 3424.9,250.85 3464.4,229 3474,223.72 3481.2,214.36 \ +3486.5,205.15", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "sequence feature relationship" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2594.1,251.78 2613.1,249.87 2632.8,248.16 2651.4,247 2706.9,243.54 3602.2,254.78 3651.4,229 3661.6,223.66 3669.6,\ +213.98 3675.4,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "sequence feature relationship" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.76 2594.1,251.74 2613.1,249.84 2632.8,248.13 2651.4,247 2683.5,245.04 3779.7,243.51 3808.4,229 3818.9,223.7 3827.2,\ +214.03 3833.4,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "sequence feature relationship" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.78 2593.6,251.75 2612.8,249.84 2632.7,248.13 2651.4,247 2687.6,244.82 3925.9,245.15 3958.4,229 3969.1,223.68 3977.8,\ +213.86 3984.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "sequence feature relationship" -> "object label closure" [color=blue, + label="object label closure", + lp="4215.9,221.5", + pos="e,4160.1,195.8 2593.6,251.73 2612.8,249.82 2632.7,248.11 2651.4,247 2692.4,244.57 4091.5,247 4128.4,229 4139.3,223.7 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "sequence feature relationship" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.5,196.31 2593.6,251.71 2612.8,249.8 2632.7,248.1 2651.4,247 2696.8,244.33 4248.4,248.69 4289.4,229 4300.2,223.79 4309.2,214.18 \ +4315.9,204.77", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "sequence feature relationship" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1644.1,251.76 1663.1,249.86 1682.8,248.15 1701.4,247 1730.5,245.2 2730,249.78 2750.4,229 2756.6,222.69 2756.6,213.66 \ -2754.2,205", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2593.6,251.7 2612.8,249.79 2632.7,248.09 2651.4,247 2676.4,245.54 4432.8,244.59 4452.4,229 4459.2,223.54 4462.6,\ +214.93 4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "sequence feature relationship" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.87 1644.1,251.75 1663.1,249.85 1682.8,248.14 1701.4,247 1761.9,243.27 2736.6,252.66 2792.4,229 2804.9,223.68 2816,213.59 \ -2824.5,203.85", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2593.6,251.69 2612.8,249.79 2632.7,248.09 2651.4,247 2702.6,244.02 4449.8,245.4 4498.4,229 4514.6,223.53 4530.1,\ +212.51 4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "sequence feature relationship" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.76 1644.1,251.73 1663.1,249.84 1682.8,248.13 1701.4,247 1766.9,243.01 2819.8,248.69 2882.4,229 2900.4,223.34 2918,211.75 \ -2931.5,201.16", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2593.6,251.69 2612.8,249.78 2632.7,248.08 2651.4,247 2759.2,240.75 4490.4,257.84 4594.4,229 4615.1,223.25 4636,211.09 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "sequence feature relationship" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1644.1,251.72 1663.1,249.82 1682.8,248.12 1701.4,247 1771.7,242.75 2903.3,253.29 2969.4,229 3011.9,213.39 3017.1,\ -186.96 3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2593.6,251.68 2612.8,249.77 2632.7,248.08 2651.4,247 2707.8,243.74 4631.6,246.26 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1748.4,265", + pos="2698.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1879.4,265", + pos="2829.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "sequence feature relationship_subject" [color=blue, height=0.5, label="nucleic acid entity", - pos="2067.4,265", + pos="3017.4,265", width=2.6539]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "sequence feature relationship_object" [color=blue, height=0.5, label="nucleic acid entity", - pos="2276.4,265", + pos="3226.4,265", width=2.6539]; } diff --git a/graphviz/sequence_feature_relationship.svg b/graphviz/sequence_feature_relationship.svg index 0a53b310d7..03e2525206 100644 --- a/graphviz/sequence_feature_relationship.svg +++ b/graphviz/sequence_feature_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + sequence feature relationship - -sequence feature relationship + +sequence feature relationship @@ -24,9 +24,9 @@ sequence feature relationship->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ sequence feature relationship->id - - -id + + +id @@ -50,9 +50,9 @@ sequence feature relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ sequence feature relationship->name - - -name + + +name @@ -76,9 +76,9 @@ sequence feature relationship->description - - -description + + +description @@ -89,9 +89,9 @@ sequence feature relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ sequence feature relationship->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ sequence feature relationship->negated - - -negated + + +negated @@ -128,9 +128,9 @@ sequence feature relationship->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ sequence feature relationship->publications - - -publications + + +publications @@ -154,9 +154,9 @@ sequence feature relationship->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ sequence feature relationship->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ sequence feature relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ sequence feature relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ sequence feature relationship->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ sequence feature relationship->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ sequence feature relationship->original predicate - - -original predicate + + +original predicate original object - -string + +string sequence feature relationship->original object - - -original object + + +original object - + +subject category + +ontology class + + + +sequence feature relationship->subject category + + +subject category + + + +object category + +ontology class + + + +sequence feature relationship->object category + + +object category + + + +subject closure + +string + + + +sequence feature relationship->subject closure + + +subject closure + + + +object closure + +string + + + +sequence feature relationship->object closure + + +object closure + + + +subject category closure + +ontology class + + + +sequence feature relationship->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +sequence feature relationship->object category closure + + +object category closure + + + +subject namespace + +string + + + +sequence feature relationship->subject namespace + + +subject namespace + + + +object namespace + +string + + + +sequence feature relationship->object namespace + + +object namespace + + + +subject label closure + +string + + + +sequence feature relationship->subject label closure + + +subject label closure + + + +object label closure + +string + + + +sequence feature relationship->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +sequence feature relationship->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + sequence feature relationship->type - - -type + + +type - + category - -category + +category - + sequence feature relationship->category - - -category + + +category - + subject - -subject + +subject - + sequence feature relationship->subject - - -subject + + +subject - + object - -object + +object - + sequence feature relationship->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + sequence feature relationship_subject - -nucleic acid entity + +nucleic acid entity - + object->relation - - + + - + sequence feature relationship_object - -nucleic acid entity + +nucleic acid entity diff --git a/graphviz/sequence_variant_modulates_treatment_association.gv b/graphviz/sequence_variant_modulates_treatment_association.gv index 3a6a194a27..bbf3f6011a 100644 --- a/graphviz/sequence_variant_modulates_treatment_association.gv +++ b/graphviz/sequence_variant_modulates_treatment_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "sequence variant modulates treatment association" [height=0.5, label="sequence variant modulates treatment association", - pos="1542.4,265", + pos="2492.4,265", width=6.8244]; association [height=0.5, pos="62.394,178", width=1.7332]; "sequence variant modulates treatment association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1297.6,263.36 984.87,261.49 461.02,254.49 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2247.8,263.24 1710.4,261.11 459.08,253.57 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "sequence variant modulates treatment association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1301.6,261.3 1018.4,257.31 565.19,248.12 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,\ -194.16 219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2248.8,262.47 1734.7,258.87 571.3,248.65 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "sequence variant modulates treatment association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1306.9,259.85 1053.2,254.69 666.18,244.59 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,\ -194.19 324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2249.7,262.06 1757.9,257.79 676.02,246.53 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ +194.18 325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "sequence variant modulates treatment association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1306.5,259.92 1076.9,255.07 744.65,245.49 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2249.3,262.37 1776.5,258.79 765.71,248.9 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "sequence variant modulates treatment association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1304.9,260.27 1103.1,255.93 829.41,246.91 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2248.3,262.93 1796.6,260.4 862.33,252.38 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "sequence variant modulates treatment association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1316.4,257.85 1154.8,252.39 951.65,243.07 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2249.1,262.31 1828.8,258.85 998.8,249.52 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "sequence variant modulates treatment association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1317.8,257.65 1229.1,252.77 1126.5,244.16 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2246.5,264.77 1894.8,264.72 1265.8,260.05 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "sequence variant modulates treatment association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1363.3,252.67 1302.5,247.33 1234.2,239.71 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2248.1,262.99 1929.3,260.71 1388.7,253.27 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "sequence variant modulates treatment association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1408.3,249.9 1369.1,244.62 1326.3,237.72 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2248.2,263.03 1959.1,260.76 1495.3,253.31 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "sequence variant modulates treatment association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1461.7,247.96 1439.6,242.75 1415.9,236.38 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2248.4,262.85 1990.8,260.37 1602.2,252.67 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "sequence variant modulates treatment association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461.1,195.6 1522,246.8 1506.7,233.96 1485.7,216.27 1468.9,202.19", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2251.6,261.36 2032.5,257.71 1725.7,249.09 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "sequence variant modulates treatment association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.7,246.95 1579,241.56 1587.8,235.35 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2246.9,264.08 2064.2,261.99 1830.9,254.16 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "sequence variant modulates treatment association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1651.7,248.87 1682,243.65 1714.7,237.04 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2264.5,258.27 2095.1,252.86 1891,243.41 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,8 +140,8 @@ digraph { width=3.015]; "sequence variant modulates treatment association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.5,195.15 1718.5,252.43 1829.8,244.7 1957.4,234.9 1983.4,229 2013.2,222.24 2045.2,209.99 2070,199.31", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2266,257.95 2175.3,253.13 2088.6,244.49 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -150,9 +150,8 @@ digraph { width=1.5346]; "sequence variant modulates treatment association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.74 1712.8,252.01 1741,250.2 1770,248.46 1797.4,247 1847.5,244.33 2202.8,249.82 2248.4,229 2260.4,223.51 2270.8,213.39 \ -2278.8,203.68", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2348.1,250.32 2324.8,245.29 2305.6,238.4 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -161,9 +160,8 @@ digraph { width=1.0652]; "sequence variant modulates treatment association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.21 1711.4,251.93 1740.1,250.11 1769.6,248.39 1797.4,247 1857.9,243.98 2285.4,249.45 2342.4,229 2351.2,225.84 2368.1,\ -212.71 2382.5,200.7", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2397.2,248.35 2388.3,243.45 2380.5,237.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -172,85 +170,201 @@ digraph { width=1.5887]; "sequence variant modulates treatment association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.23 1710.4,251.84 1739.4,250.01 1769.3,248.31 1797.4,247 1835.4,245.24 2447.4,245.92 2481.4,229 2492.1,223.7 2500.8,\ -214.07 2507.4,204.67", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.97 1709.3,251.79 1738.7,249.95 1768.9,248.26 1797.4,247 1820.5,245.98 2611,241.7 2630.4,229 2638.5,223.67 2643.8,214.68 \ -2647.3,205.78", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2591,248.4 2601.8,243.53 2612,237.21 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "sequence variant modulates treatment association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2653.8,251.39 2690,246.2 2722.1,238.99 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "sequence variant modulates treatment association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.4,195.77 2668.5,252.44 2759.4,245.65 2855.5,236.88 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "sequence variant modulates treatment association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.16 2667.2,252.32 2819.6,242.14 3016.4,229 3016.4,229 3030.2,223.21 3042.9,212.56 3052.7,202.58", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "sequence variant modulates treatment association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.32 2663.5,252.07 2691.5,250.27 2720.3,248.51 2747.4,247 2769.9,245.75 3134,242.04 3152.4,229 3160,223.63 3164.7,214.92 \ +3167.6,206.26", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "sequence variant modulates treatment association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.16 2661.7,251.95 2690.3,250.13 2719.7,248.4 2747.4,247 2776.3,245.54 3242.8,242.48 3268.4,229 3278.5,223.67 3286.6,\ +214.17 3292.6,204.87", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "sequence variant modulates treatment association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.15 2660,251.83 2689.1,250 2719.1,248.3 2747.4,247 2787.2,245.17 3429.5,248.32 3464.4,229 3473.9,223.7 3481.2,214.34 \ +3486.5,205.14", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "sequence variant modulates treatment association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2659,251.77 2688.4,249.93 2718.8,248.24 2747.4,247 2797.6,244.83 3606.9,252.34 3651.4,229 3661.6,223.65 3669.6,213.96 \ +3675.4,204.53", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "sequence variant modulates treatment association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.75 2658.6,251.72 2688.2,249.88 2718.7,248.2 2747.4,247 2776.8,245.77 3782.1,242.32 3808.4,229 3818.9,223.7 3827.2,214.02 \ +3833.4,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "sequence variant modulates treatment association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.77 2658.3,251.69 2688,249.85 2718.6,248.17 2747.4,247 2781,245.63 3928.3,243.98 3958.4,229 3969.1,223.67 3977.8,213.85 \ +3984.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "sequence variant modulates treatment association" -> "object label closure" [color=blue, + label="object label closure", + lp="4215.9,221.5", + pos="e,4160.1,195.79 2658,251.67 2687.7,249.82 2718.5,248.15 2747.4,247 2785.7,245.47 4093.9,245.84 4128.4,229 4139.3,223.69 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "sequence variant modulates treatment association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.5,196.3 2657.6,251.66 2687.5,249.8 2718.4,248.14 2747.4,247 2790.2,245.32 4250.8,247.55 4289.4,229 4300.2,223.79 4309.2,214.18 \ +4315.9,204.76", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "sequence variant modulates treatment association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1709,251.75 1738.4,249.91 1768.8,248.22 1797.4,247 1823.8,245.87 2731.9,247.9 2750.4,229 2756.6,222.69 2756.5,213.65 \ -2754.2,204.99", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2657.3,251.65 2687.2,249.79 2718.2,248.12 2747.4,247 2771.1,246.09 4433.9,243.76 4452.4,229 4459.2,223.54 4462.6,\ +214.92 4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "sequence variant modulates treatment association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.86 1709,251.73 1738.4,249.89 1768.8,248.21 1797.4,247 1852.6,244.66 2741.5,250.62 2792.4,229 2804.9,223.67 2816,213.58 \ -2824.5,203.84", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2657.3,251.64 2687.2,249.79 2718.2,248.12 2747.4,247 2796,245.13 4452.3,244.56 4498.4,229 4514.6,223.53 4530.1,212.5 \ +4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "sequence variant modulates treatment association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.75 1708.6,251.71 1738.2,249.87 1768.7,248.19 1797.4,247 1857.6,244.49 2824.9,247.13 2882.4,229 2900.4,223.32 2918,211.74 \ -2931.5,201.15", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2657.3,251.63 2687.2,249.78 2718.2,248.11 2747.4,247 2849.9,243.09 4495.5,256.44 4594.4,229 4615.1,223.24 4636,211.08 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "sequence variant modulates treatment association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1708.3,251.7 1738,249.86 1768.6,248.18 1797.4,247 1862.5,244.33 2908.3,251.49 2969.4,229 3011.9,213.37 3017.1,186.96 \ -3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2657.3,251.62 2687.2,249.77 2718.2,248.11 2747.4,247 2801.2,244.96 4634.1,245.46 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1844.4,265", + pos="2794.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1975.4,265", + pos="2925.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "sequence variant modulates treatment association_subject" [color=blue, height=0.5, label="sequence variant", - pos="2158.4,265", + pos="3108.4,265", width=2.5095]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "sequence variant modulates treatment association_object" [color=blue, height=0.5, label=treatment, - pos="2324.4,265", + pos="3274.4,265", width=1.6068]; } diff --git a/graphviz/sequence_variant_modulates_treatment_association.svg b/graphviz/sequence_variant_modulates_treatment_association.svg index f45590a50e..82165947a2 100644 --- a/graphviz/sequence_variant_modulates_treatment_association.svg +++ b/graphviz/sequence_variant_modulates_treatment_association.svg @@ -4,16 +4,16 @@ - + %3 - + sequence variant modulates treatment association - -sequence variant modulates treatment association + +sequence variant modulates treatment association @@ -24,9 +24,9 @@ sequence variant modulates treatment association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ sequence variant modulates treatment association->id - - -id + + +id @@ -50,9 +50,9 @@ sequence variant modulates treatment association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ sequence variant modulates treatment association->name - - -name + + +name @@ -76,9 +76,9 @@ sequence variant modulates treatment association->description - - -description + + +description @@ -89,9 +89,9 @@ sequence variant modulates treatment association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ sequence variant modulates treatment association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ sequence variant modulates treatment association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ sequence variant modulates treatment association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ sequence variant modulates treatment association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ sequence variant modulates treatment association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ sequence variant modulates treatment association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ sequence variant modulates treatment association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ sequence variant modulates treatment association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ sequence variant modulates treatment association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ sequence variant modulates treatment association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ sequence variant modulates treatment association->original predicate - - -original predicate + + +original predicate original object - -string + +string sequence variant modulates treatment association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +sequence variant modulates treatment association->subject category + + +subject category + + + +object category + +ontology class + + + +sequence variant modulates treatment association->object category + + +object category + + + +subject closure + +string + + + +sequence variant modulates treatment association->subject closure + + +subject closure + + + +object closure + +string + + + +sequence variant modulates treatment association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +sequence variant modulates treatment association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +sequence variant modulates treatment association->object category closure + + +object category closure + + + +subject namespace + +string + + + +sequence variant modulates treatment association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +sequence variant modulates treatment association->object namespace + + +object namespace + + + +subject label closure + +string + + + +sequence variant modulates treatment association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +sequence variant modulates treatment association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +sequence variant modulates treatment association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + sequence variant modulates treatment association->type - - -type + + +type - + category - -category + +category - + sequence variant modulates treatment association->category - - -category + + +category - + subject - -subject + +subject - + sequence variant modulates treatment association->subject - - -subject + + +subject - + object - -object + +object - + sequence variant modulates treatment association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + sequence variant modulates treatment association_subject - -sequence variant + +sequence variant - + object->relation - - + + - + sequence variant modulates treatment association_object - -treatment + +treatment diff --git a/graphviz/taxon_to_taxon_association.gv b/graphviz/taxon_to_taxon_association.gv index e7bdce5e0a..ea2af3caff 100644 --- a/graphviz/taxon_to_taxon_association.gv +++ b/graphviz/taxon_to_taxon_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3064.4,283"]; + graph [bb="0,0,4788.4,283"]; node [label="\N"]; "taxon to taxon association" [height=0.5, label="taxon to taxon association", - pos="1542.4,265", + pos="2492.4,265", width=3.665]; association [height=0.5, pos="62.394,178", width=1.7332]; "taxon to taxon association" -> association [label=is_a, - lp="283.39,221.5", - pos="e,103.54,191.64 1410.7,263.87 1131.3,263.03 486.71,257.91 269.39,229 215.28,221.8 154.72,206.27 113.16,194.42"]; + lp="281.39,221.5", + pos="e,103.12,191.79 2360.8,263.64 1914.4,262.2 474.2,255.51 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "taxon to taxon association" -> id [color=blue, label=id, - lp="403.39,221.5", - pos="e,210.11,189.94 1411,262.71 1153.2,259.72 589.24,250.85 396.39,229 321.22,220.48 302.36,216.02 229.39,196 226.24,195.13 222.99,194.16 \ -219.75,193.14", + lp="398.39,221.5", + pos="e,210.38,190 2360.7,263.22 1931,260.47 585.98,250.26 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ +219.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "taxon to taxon association" -> iri [color=blue, label=iri, - lp="527.39,221.5", - pos="e,314.99,190.21 1412.1,261.87 1176.5,257.63 688.49,246.96 519.39,229 436.78,220.22 416.02,216.07 335.39,196 331.96,195.15 328.43,\ -194.19 324.89,193.17", + lp="515.39,221.5", + pos="e,315.29,190.23 2361.2,263 1948,259.65 690.32,248.02 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,194.18 \ +325.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "taxon to taxon association" -> name [color=blue, label=name, - lp="636.39,221.5", - pos="e,441.37,190.85 1412,261.97 1194.3,258.09 766.19,248.26 616.39,229 558.92,221.61 494.32,205.5 451.08,193.56", + lp="627.39,221.5", + pos="e,440.01,191.15 2360.8,263.18 1961.4,260.46 779.67,250.65 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "taxon to taxon association" -> description [color=blue, label=description, - lp="761.89,221.5", - pos="e,590.6,193.5 1411.6,262.29 1214.4,259.06 850.17,250.35 721.39,229 679.68,222.08 633.76,208.18 600.17,196.79", + lp="755.89,221.5", + pos="e,588.8,193.65 2360.9,263.5 1977.1,261.76 876,254.56 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "taxon to taxon association" -> "has attribute" [color=blue, label="has attribute", - lp="915.39,221.5", - pos="e,730.76,191.55 1413.7,260.86 1248.1,256.19 969.63,246.11 868.39,229 824.02,221.5 774.85,206.5 740.49,194.88", + lp="913.39,221.5", + pos="e,729.98,191.75 2360.9,263.17 2000.1,260.59 1011.9,251.56 866.39,229 822.26,222.16 773.51,207 739.58,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "taxon to taxon association" -> predicate [color=blue, label=predicate, - lp="1068.4,221.5", - pos="e,888.04,193 1412.4,261.78 1309.3,258.4 1161.9,249.97 1034.4,229 987.59,221.3 935.56,207.21 897.8,195.94", + lp="1074.4,221.5", + pos="e,887.81,193.09 2360.4,264.62 2052.3,265.46 1292.9,263.8 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "taxon to taxon association" -> negated [color=blue, label=negated, - lp="1201.4,221.5", - pos="e,1021.7,190.34 1422.6,257.37 1349.9,252.18 1255.4,243.37 1172.4,229 1123.6,220.54 1068.9,204.99 1031.7,193.47", + lp="1220.4,221.5", + pos="e,1022.3,190.23 2360.8,263.65 2076.9,262.38 1414.5,256.46 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "taxon to taxon association" -> qualifiers [color=blue, label=qualifiers, - lp="1320.9,221.5", - pos="e,1168.1,193.53 1439,253.82 1392.4,248.2 1336.8,240.07 1287.4,229 1250.1,220.63 1208.9,207.57 1177.8,196.9", + lp="1356.9,221.5", + pos="e,1171.6,193.02 2360.6,263.72 2098.4,262.55 1520,256.8 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "taxon to taxon association" -> publications [color=blue, label=publications, - lp="1438.4,221.5", - pos="e,1314.4,194.2 1470.1,249.9 1445.7,244.37 1418.6,237.33 1394.4,229 1370.1,220.66 1344,208.78 1323.4,198.69", + lp="1499.4,221.5", + pos="e,1321.9,192.66 2360.5,263.68 2121.5,262.42 1625.7,256.46 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "taxon to taxon association" -> "has evidence" [color=blue, label="has evidence", - lp="1544.9,221.5", - pos="e,1461,195.47 1522.4,247.21 1507.1,234.32 1485.8,216.38 1468.9,202.13", + lp="1652.9,221.5", + pos="e,1479.4,193.55 2361.1,262.91 2150.8,260.47 1747.5,252.76 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "taxon to taxon association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1675.9,221.5", - pos="e,1628.7,196.14 1570.2,247.31 1578.6,241.84 1587.6,235.49 1595.4,229 1604.6,221.33 1613.9,212.07 1621.8,203.61", + lp="1802.9,221.5", + pos="e,1667.9,195.78 2360.3,264.76 2176,264.63 1851.7,259.81 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "taxon to taxon association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1884.4,221.5", - pos="e,1841.2,195.02 1633.4,251.9 1668.4,246.3 1708.6,238.69 1744.4,229 1774,220.97 1806.3,209.03 1831.8,198.83", + lp="1972.4,221.5", + pos="e,1872.6,196 2363.4,261.13 2188,256.58 1893.8,246.39 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "taxon to taxon association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2137.9,221.5", - pos="e,2079.8,195.22 1634.5,252.09 1650.7,250.22 1667.6,248.43 1683.4,247 1816.4,235 1852.9,257.31 1983.4,229 2013.5,222.48 2045.8,210.09 \ -2070.6,199.27", + lp="2180.9,221.5", + pos="e,2087.6,195.53 2362.4,261.8 2247.1,258.46 2093.8,250.07 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "taxon to taxon association" -> timepoint [color=blue, label=timepoint, - lp="2303.4,221.5", - pos="e,2284.9,195.77 1632.9,251.89 1649.7,249.99 1667,248.24 1683.4,247 1746,242.24 2191.1,254.85 2248.4,229 2260.4,223.56 2270.9,213.45 \ -2278.8,203.73", + lp="2332.4,221.5", + pos="e,2291.1,196.26 2379.2,255.75 2342.9,250.63 2309,242.36 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "taxon to taxon association" -> "original subject" [color=blue, label="original subject", - lp="2422.4,221.5", - pos="e,2390.2,194.23 1632.9,251.83 1649.7,249.93 1667,248.21 1683.4,247 1756.4,241.61 2273.4,253.53 2342.4,229 2351.2,225.86 2368.2,212.73 \ -2382.5,200.72", + lp="2430.4,221.5", + pos="e,2387.4,193.75 2403.7,251.67 2392.3,246.41 2381.9,239.1 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,203 @@ digraph { width=1.5887]; "taxon to taxon association" -> "original predicate" [color=blue, label="original predicate", - lp="2562.9,221.5", - pos="e,2512.8,196.24 1632.5,251.81 1649.4,249.9 1666.9,248.18 1683.4,247 1727.6,243.84 2441.6,248.66 2481.4,229 2492.1,223.72 2500.8,\ -214.09 2507.4,204.69", + lp="2556.9,221.5", + pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2653.4,178", + pos="2635.4,178", width=1.0652]; "taxon to taxon association" -> "original object" [color=blue, label="original object", - lp="2694.9,221.5", - pos="e,2650.4,195.98 1632.2,251.8 1649.1,249.88 1666.8,248.16 1683.4,247 1709.6,245.17 2608.4,243.4 2630.4,229 2638.5,223.68 2643.8,214.69 \ -2647.3,205.79", + lp="2681.9,221.5", + pos="e,2634.3,196.46 2582.6,251.85 2596.6,246.63 2609.8,239.3 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2768.4,178", + width=2.1304]; + "taxon to taxon association" -> "subject category" [color=blue, + label="subject category", + lp="2811.9,221.5", + pos="e,2762.2,196.16 2587,252.37 2653.1,243.92 2730.9,233.26 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="2939.4,178", + width=2.1304]; + "taxon to taxon association" -> "object category" [color=blue, + label="object category", + lp="2956.9,221.5", + pos="e,2923.7,195.62 2585.2,252.19 2601.3,250.33 2617.8,248.52 2633.4,247 2687.1,241.77 2825.1,248.44 2875.4,229 2890.4,223.19 2904.8,\ +212.61 2916.1,202.67", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3072.4,178", + width=1.0652]; + "taxon to taxon association" -> "subject closure" [color=blue, + label="subject closure", + lp="3093.9,221.5", + pos="e,3059.6,195.26 2584.1,251.96 2600.5,250.09 2617.4,248.34 2633.4,247 2675.8,243.45 2977,245.11 3016.4,229 3030.2,223.34 3042.9,212.71 \ +3052.7,202.7", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3172.4,178", + width=1.0652]; + "taxon to taxon association" -> "object closure" [color=blue, + label="object closure", + lp="3214.4,221.5", + pos="e,3170.3,196.35 2583.3,251.88 2599.9,250 2617.2,248.26 2633.4,247 2662.2,244.77 3128.8,245.59 3152.4,229 3160.1,223.61 3164.8,214.77 \ +3167.7,206.02", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3305.4,178", + width=2.1304]; + "taxon to taxon association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3372.9,221.5", + pos="e,3297.7,196.19 2582.9,251.84 2599.7,249.95 2617,248.21 2633.4,247 2668.6,244.39 3237.1,245.33 3268.4,229 3278.6,223.7 3286.6,214.2 \ +3292.6,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3497.4,178", + width=2.1304]; + "taxon to taxon association" -> "object category closure" [color=blue, + label="object category closure", + lp="3563.9,221.5", + pos="e,3491.1,196.16 2582.5,251.8 2599.4,249.89 2616.9,248.17 2633.4,247 2679.5,243.73 3424,251.32 3464.4,229 3474,223.72 3481.2,214.36 \ +3486.5,205.16", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3687.4,178", + width=1.0652]; + "taxon to taxon association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3736.4,221.5", + pos="e,3680.3,195.72 2582.1,251.78 2599.1,249.87 2616.8,248.14 2633.4,247 2689.8,243.11 3601.3,255.23 3651.4,229 3661.6,223.66 3669.6,\ +213.98 3675.4,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="3846.4,178", + width=1.0652]; + "taxon to taxon association" -> "object namespace" [color=blue, + label="object namespace", + lp="3890.4,221.5", + pos="e,3838.7,195.76 2582.1,251.75 2599.1,249.84 2616.8,248.13 2633.4,247 2666,244.79 3779.3,243.73 3808.4,229 3818.9,223.71 3827.2,214.03 \ +3833.4,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="3997.4,178", + width=1.0652]; + "taxon to taxon association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4050.4,221.5", + pos="e,3989.4,195.78 2582.1,251.73 2599.1,249.82 2616.8,248.11 2633.4,247 2670.1,244.54 3925.4,245.37 3958.4,229 3969.1,223.68 3977.8,\ +213.86 3984.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4168.4,178", + width=1.0652]; + "taxon to taxon association" -> "object label closure" [color=blue, + label="object label closure", + lp="4215.9,221.5", + pos="e,4160.1,195.8 2581.8,251.75 2598.9,249.82 2616.7,248.11 2633.4,247 2674.8,244.26 4091.1,247.22 4128.4,229 4139.3,223.7 4148.1,213.88 \ +4154.7,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4330.4,178", + width=2.347]; + "taxon to taxon association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4378.9,221.5", + pos="e,4321.5,196.31 2581.8,251.73 2598.9,249.81 2616.7,248.1 2633.4,247 2679.3,243.99 4247.9,248.9 4289.4,229 4300.2,223.79 4309.2,214.18 \ +4315.9,204.77", style=solid]; type [height=0.5, - pos="2741.4,178", + pos="4464.4,178", width=0.86659]; "taxon to taxon association" -> type [color=blue, label=type, - lp="2772.4,221.5", - pos="e,2750.8,195.54 1632.1,251.77 1649.1,249.86 1666.8,248.14 1683.4,247 1713,244.97 2729.6,250.14 2750.4,229 2756.6,222.69 2756.6,213.66 \ -2754.2,205", + lp="4478.4,221.5", + pos="e,4465.2,196.18 2581.8,251.72 2598.9,249.8 2616.7,248.09 2633.4,247 2658.6,245.36 4432.6,244.74 4452.4,229 4459.2,223.54 4462.6,\ +214.93 4464.1,206.37", style=solid]; category [height=0.5, - pos="2842.4,178", + pos="4565.4,178", width=1.4263]; "taxon to taxon association" -> category [color=blue, label=category, - lp="2846.9,221.5", - pos="e,2831,195.87 1632.1,251.76 1649.1,249.85 1666.8,248.13 1683.4,247 1744.9,242.81 2735.7,253.04 2792.4,229 2804.9,223.69 2816,213.59 \ -2824.5,203.85", + lp="4558.9,221.5", + pos="e,4549.8,195.25 2581.8,251.72 2598.9,249.79 2616.7,248.09 2633.4,247 2685.1,243.64 4449.3,245.56 4498.4,229 4514.6,223.53 4530.1,\ +212.51 4542.1,202.2", style=solid]; subject [height=0.5, - pos="2956.4,178", + pos="4679.4,178", width=1.2277]; "taxon to taxon association" -> subject [color=blue, label=subject, - lp="2939.4,221.5", - pos="e,2939.4,194.76 1632.1,251.75 1649.1,249.84 1666.8,248.12 1683.4,247 1749.9,242.51 2818.8,248.98 2882.4,229 2900.4,223.34 2918,211.76 \ -2931.5,201.16", + lp="4655.4,221.5", + pos="e,4660.1,194.33 2581.8,251.71 2598.9,249.79 2616.7,248.08 2633.4,247 2742.1,239.97 4489.4,258.11 4594.4,229 4615.1,223.25 4636,211.09 \ +4651.9,200.2", style=solid]; object [height=0.5, - pos="2999.4,91", + pos="4722.4,91", width=1.0832]; "taxon to taxon association" -> object [color=blue, label=object, - lp="3042.4,178", - pos="e,3012.8,108.09 1632.1,251.73 1649.1,249.82 1666.8,248.11 1683.4,247 1754.7,242.22 2902.3,253.63 2969.4,229 3011.9,213.39 3017.1,\ -186.96 3022.4,142 3023.2,135.38 3024.3,133.39 3022.4,127 3021.4,123.55 3019.9,120.13 3018.1,116.85", + lp="4766.4,178", + pos="e,4735.8,108.09 2581.8,251.71 2598.9,249.78 2616.7,248.08 2633.4,247 2690.3,243.33 4631.1,246.41 4685.4,229 4709.7,221.2 4718,217.1 \ +4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1730.4,265", + pos="2680.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="1861.4,265", + pos="2811.4,265", width=2.0762]; subject -> object [label=relation, - lp="2994.4,134.5", - pos="e,2981.5,107.23 2957.5,159.55 2958.7,149.57 2961.2,137.07 2966.4,127 2968.6,122.68 2971.5,118.52 2974.7,114.66"]; + lp="4717.4,134.5", + pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; relation [height=0.5, - pos="2944.4,18", + pos="4667.4,18", width=1.2999]; - subject -> relation [pos="e,2945.7,36.188 2955.1,159.79 2953,132.48 2949,78.994 2946.5,46.38", + subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", style=dotted]; "taxon to taxon association_subject" [color=blue, height=0.5, label="organism taxon", - pos="2037.4,265", + pos="2987.4,265", width=2.3109]; - object -> relation [pos="e,2957.2,35.54 2986.9,73.889 2980,64.939 2971.2,53.617 2963.4,43.584", + object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", style=dotted]; "taxon to taxon association_object" [color=blue, height=0.5, label="organism taxon", - pos="2221.4,265", + pos="3171.4,265", width=2.3109]; } diff --git a/graphviz/taxon_to_taxon_association.svg b/graphviz/taxon_to_taxon_association.svg index 45275dfc8e..b2865df1be 100644 --- a/graphviz/taxon_to_taxon_association.svg +++ b/graphviz/taxon_to_taxon_association.svg @@ -4,16 +4,16 @@ - + %3 - + taxon to taxon association - -taxon to taxon association + +taxon to taxon association @@ -24,9 +24,9 @@ taxon to taxon association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ taxon to taxon association->id - - -id + + +id @@ -50,9 +50,9 @@ taxon to taxon association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ taxon to taxon association->name - - -name + + +name @@ -76,9 +76,9 @@ taxon to taxon association->description - - -description + + +description @@ -89,9 +89,9 @@ taxon to taxon association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ taxon to taxon association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ taxon to taxon association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ taxon to taxon association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ taxon to taxon association->publications - - -publications + + +publications @@ -154,9 +154,9 @@ taxon to taxon association->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ taxon to taxon association->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ taxon to taxon association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ taxon to taxon association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ taxon to taxon association->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ taxon to taxon association->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ taxon to taxon association->original predicate - - -original predicate + + +original predicate original object - -string + +string taxon to taxon association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +taxon to taxon association->subject category + + +subject category + + + +object category + +ontology class + + + +taxon to taxon association->object category + + +object category + + + +subject closure + +string + + + +taxon to taxon association->subject closure + + +subject closure + + + +object closure + +string + + + +taxon to taxon association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +taxon to taxon association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +taxon to taxon association->object category closure + + +object category closure + + + +subject namespace + +string + + + +taxon to taxon association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +taxon to taxon association->object namespace + + +object namespace + + + +subject label closure + +string + + + +taxon to taxon association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +taxon to taxon association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +taxon to taxon association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + taxon to taxon association->type - - -type + + +type - + category - -category + +category - + taxon to taxon association->category - - -category + + +category - + subject - -subject + +subject - + taxon to taxon association->subject - - -subject + + +subject - + object - -object + +object - + taxon to taxon association->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + taxon to taxon association_subject - -organism taxon + +organism taxon - + object->relation - - + + - + taxon to taxon association_object - -organism taxon + +organism taxon diff --git a/graphviz/transcript_to_gene_relationship.gv b/graphviz/transcript_to_gene_relationship.gv index f8fb7d0d6d..b13a425a40 100644 --- a/graphviz/transcript_to_gene_relationship.gv +++ b/graphviz/transcript_to_gene_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,3238.5,283"]; + graph [bb="0,0,4962.5,283"]; node [label="\N"]; "transcript to gene relationship" [height=0.5, label="transcript to gene relationship", - pos="1716.5,265", + pos="2666.5,265", width=4.2607]; "sequence feature relationship" [height=0.5, pos="149.49,178", width=4.1524]; "transcript to gene relationship" -> "sequence feature relationship" [label=is_a, - lp="457.49,221.5", - pos="e,220.1,193.89 1564.5,262.51 1275.5,259.22 656.5,249.94 443.49,229 370.79,221.85 288.92,207.4 230.08,195.86"]; + lp="455.49,221.5", + pos="e,219,194.01 2513.7,262.96 2044.9,259.58 645.91,248 441.49,229 368.99,222.26 287.38,207.69 228.91,196"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "transcript to gene relationship" -> id [color=blue, label=id, - lp="577.49,221.5", - pos="e,384.21,189.94 1564.5,262.46 1298.3,259.25 758.32,250.28 570.49,229 495.31,220.48 476.45,216.02 403.49,196 400.33,195.13 397.09,\ -194.16 393.84,193.14", + lp="572.49,221.5", + pos="e,384.47,190 2513.9,263.08 2063.1,260.15 757.01,249.92 565.49,229 492.44,221.02 474.29,215.65 403.49,196 400.38,195.14 397.18,194.17 \ +393.98,193.16", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "transcript to gene relationship" -> iri [color=blue, label=iri, - lp="701.49,221.5", - pos="e,489.09,190.21 1565.7,261.5 1323.4,257.02 857.83,246.46 693.49,229 610.87,220.22 590.11,216.07 509.49,196 506.05,195.15 502.52,\ -194.19 498.98,193.17", + lp="689.49,221.5", + pos="e,489.39,190.23 2513.9,262.82 2080.4,259.26 861.36,247.7 681.49,229 604.07,220.95 584.91,215.26 509.49,196 506.11,195.14 502.63,\ +194.18 499.14,193.17", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "transcript to gene relationship" -> name [color=blue, label=name, - lp="810.49,221.5", - pos="e,615.46,190.85 1565.5,261.6 1342.5,257.48 935.69,247.67 790.49,229 733.01,221.61 668.41,205.5 625.17,193.56", + lp="801.49,221.5", + pos="e,614.11,191.15 2513.7,263.03 2095.4,260.12 950.82,250.28 781.49,229 726.67,222.11 665.3,206.11 623.92,194.05", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "transcript to gene relationship" -> description [color=blue, label=description, - lp="935.99,221.5", - pos="e,764.69,193.5 1564.9,261.94 1363.9,258.45 1019.9,249.63 895.49,229 853.78,222.08 807.86,208.18 774.27,196.79", + lp="929.99,221.5", + pos="e,762.9,193.65 2513.4,263.4 2111.7,261.49 1047.2,254.1 889.49,229 849.13,222.58 804.89,208.66 772.54,197.14", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "transcript to gene relationship" -> "has attribute" [color=blue, label="has attribute", - lp="1089.5,221.5", - pos="e,904.86,191.55 1568.2,260.29 1401,255.41 1139.8,245.45 1042.5,229 998.11,221.5 948.94,206.5 914.58,194.88", + lp="1087.5,221.5", + pos="e,904.07,191.75 2513.9,263.01 2137.2,260.25 1183.3,251.13 1040.5,229 996.35,222.16 947.61,207 913.67,195.15", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "transcript to gene relationship" -> predicate [color=blue, label=predicate, - lp="1242.5,221.5", - pos="e,1062.1,193 1566.7,261.09 1465.1,257.3 1328,248.66 1208.5,229 1161.7,221.3 1109.7,207.21 1071.9,195.94", + lp="1248.5,221.5", + pos="e,1061.9,193.09 2512.9,264.68 2192.4,265.37 1461.3,263.01 1214.5,229 1165.3,222.22 1110.6,207.65 1071.5,195.99", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "transcript to gene relationship" -> negated [color=blue, label=negated, - lp="1375.5,221.5", - pos="e,1195.8,190.34 1581.8,256.28 1511.4,250.97 1423.9,242.4 1346.5,229 1297.6,220.54 1243,204.99 1205.8,193.47", + lp="1394.5,221.5", + pos="e,1196.4,190.23 2513.4,263.55 2218.8,262.07 1583.2,255.78 1365.5,229 1309.6,222.13 1247,205.38 1206.1,193.16", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "transcript to gene relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1495,221.5", - pos="e,1342.2,193.53 1604,252.71 1559.4,247.14 1507.7,239.36 1461.5,229 1424.2,220.63 1383,207.57 1351.9,196.9", + lp="1531,221.5", + pos="e,1345.7,193.02 2513.4,263.62 2242.4,262.23 1688.9,256.07 1497.5,229 1448.7,222.11 1394.6,207.65 1355.7,196.05", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "transcript to gene relationship" -> publications [color=blue, label=publications, - lp="1612.5,221.5", - pos="e,1488.4,194.2 1641.1,249.21 1617.6,243.79 1591.7,236.98 1568.5,229 1544.2,220.66 1518.1,208.78 1497.5,198.69", + lp="1673.5,221.5", + pos="e,1496,192.66 2513.4,263.56 2267.4,262.06 1794.9,255.67 1629.5,229 1586.6,222.09 1539.4,207.61 1505.6,196.01", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=2.0943]; "transcript to gene relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1719,221.5", - pos="e,1635.2,195.6 1696,246.8 1680.8,233.96 1659.8,216.27 1643,202.19", + lp="1827,221.5", + pos="e,1653.5,193.55 2514.3,262.66 2299.1,259.95 1917,251.99 1780.5,229 1740.1,222.2 1695.7,208.38 1663.2,196.99", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -120,8 +120,8 @@ digraph { width=3.015]; "transcript to gene relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1850,221.5", - pos="e,1802.8,196.14 1744.5,247.13 1752.9,241.7 1761.8,235.42 1769.5,229 1778.7,221.33 1788,212.07 1795.9,203.61", + lp="1977,221.5", + pos="e,1842,195.78 2513,264.72 2326,264.23 2021.6,258.65 1912.5,229 1890.7,223.09 1868.3,211.61 1850.8,201.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -130,8 +130,8 @@ digraph { width=3.015]; "transcript to gene relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2058.5,221.5", - pos="e,2015.3,195.02 1813.1,251 1846.8,245.49 1884.6,238.18 1918.5,229 1948.1,220.97 1980.4,209.03 2005.9,198.83", + lp="2146.5,221.5", + pos="e,2046.7,196 2517.6,260.6 2340.7,255.81 2067.3,245.75 2051.5,229 2045.7,222.9 2044.5,214.27 2045.1,205.9", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -140,9 +140,8 @@ digraph { width=3.015]; "transcript to gene relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2312,221.5", - pos="e,2253.9,195.17 1824.3,252.16 1842.7,250.3 1861.6,248.51 1879.5,247 2002.9,236.58 2036.5,255.53 2157.5,229 2187.5,222.41 2219.8,\ -210.02 2244.7,199.22", + lp="2355,221.5", + pos="e,2261.7,195.53 2516.4,261.18 2404,257.46 2266.8,248.87 2248.5,229 2240.8,220.62 2245.7,210.86 2254.2,202.2", style=solid]; timepoint [color=blue, height=0.5, @@ -151,9 +150,8 @@ digraph { width=1.5346]; "transcript to gene relationship" -> timepoint [color=blue, label=timepoint, - lp="2477.5,221.5", - pos="e,2459,195.77 1822,251.89 1841.1,250.01 1860.9,248.28 1879.5,247 1939.7,242.87 2367.5,253.88 2422.5,229 2434.5,223.55 2445,213.44 \ -2452.9,203.72", + lp="2506.5,221.5", + pos="e,2465.2,196.26 2543.3,254.25 2510.9,249.06 2482,241.12 2471.5,229 2466.1,222.83 2464.4,214.43 2464.4,206.27", style=solid]; "original subject" [color=blue, height=0.5, @@ -162,9 +160,8 @@ digraph { width=1.0652]; "transcript to gene relationship" -> "original subject" [color=blue, label="original subject", - lp="2596.5,221.5", - pos="e,2564.3,194.22 1821.6,251.86 1840.8,249.97 1860.7,248.24 1879.5,247 1950.1,242.32 2449.8,252.74 2516.5,229 2525.3,225.86 2542.2,\ -212.73 2556.6,200.71", + lp="2604.5,221.5", + pos="e,2561.4,193.75 2575.2,250.43 2564.8,245.28 2555.5,238.33 2548.5,229 2541.8,220.01 2546.6,209.73 2554.4,200.83", style=solid]; "original predicate" [color=blue, height=0.5, @@ -173,85 +170,204 @@ digraph { width=1.5887]; "transcript to gene relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2737,221.5", - pos="e,2686.9,196.24 1821.2,251.82 1840.5,249.93 1860.6,248.2 1879.5,247 1922.5,244.26 2616.8,248.13 2655.5,229 2666.2,223.71 2674.9,\ -214.09 2681.5,204.69", + lp="2731,221.5", + pos="e,2678.7,195.4 2664.1,246.84 2663.5,236.95 2663.7,224.45 2667.5,214 2668.8,210.42 2670.6,206.94 2672.7,203.64", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2827.5,178", + pos="2809.5,178", width=1.0652]; "transcript to gene relationship" -> "original object" [color=blue, label="original object", - lp="2869,221.5", - pos="e,2824.5,195.98 1821.2,251.76 1840.5,249.87 1860.6,248.17 1879.5,247 1905.1,245.42 2783,243.07 2804.5,229 2812.6,223.68 2817.9,214.69 \ -2821.4,205.79", + lp="2856,221.5", + pos="e,2808.4,196.46 2759.9,250.58 2772.7,245.47 2784.8,238.49 2794.5,229 2800.6,223.04 2804.2,214.69 2806.4,206.52", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="2942.5,178", + width=2.1304]; + "transcript to gene relationship" -> "subject category" [color=blue, + label="subject category", + lp="2986,221.5", + pos="e,2936.3,196.16 2777.3,252.5 2836.6,245.58 2899.8,236.65 2911.5,229 2920.2,223.28 2927,214.13 2931.9,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3113.5,178", + width=2.1304]; + "transcript to gene relationship" -> "object category" [color=blue, + label="object category", + lp="3131,221.5", + pos="e,3097.6,195.83 2775.6,252.28 2793.6,250.44 2812.1,248.62 2829.5,247 2878.3,242.46 3003.8,246.85 3049.5,229 3064.4,223.18 3078.7,\ +212.7 3089.9,202.83", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3246.5,178", + width=1.0652]; + "transcript to gene relationship" -> "subject closure" [color=blue, + label="subject closure", + lp="3268,221.5", + pos="e,3233.7,195.25 2773.4,252.02 2792.1,250.16 2811.3,248.4 2829.5,247 2869.5,243.92 3153.3,244.24 3190.5,229 3204.3,223.32 3217,212.69 \ +3226.8,202.68", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3346.5,178", + width=1.0652]; + "transcript to gene relationship" -> "object closure" [color=blue, + label="object closure", + lp="3388.5,221.5", + pos="e,3344.4,196.34 2772.1,251.94 2791.1,250.05 2810.9,248.3 2829.5,247 2857,245.07 3303.9,244.9 3326.5,229 3334.2,223.6 3338.9,214.77 \ +3341.8,206.01", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3479.5,178", + width=2.1304]; + "transcript to gene relationship" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3547,221.5", + pos="e,3471.8,196.18 2771.6,251.87 2790.8,249.99 2810.8,248.25 2829.5,247 2863.5,244.73 3412.3,244.78 3442.5,229 3452.6,223.69 3460.7,\ +214.2 3466.7,204.9", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3671.5,178", + width=2.1304]; + "transcript to gene relationship" -> "object category closure" [color=blue, + label="object category closure", + lp="3738,221.5", + pos="e,3665.2,196.16 2771.2,251.81 2790.5,249.91 2810.6,248.19 2829.5,247 2874.4,244.17 3599.1,250.74 3638.5,229 3648,223.72 3655.3,214.36 \ +3660.6,205.15", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="3861.5,178", + width=1.0652]; + "transcript to gene relationship" -> "subject namespace" [color=blue, + label="subject namespace", + lp="3910.5,221.5", + pos="e,3854.4,195.72 2770.7,251.78 2790.2,249.88 2810.5,248.16 2829.5,247 2884.7,243.63 3776.5,254.67 3825.5,229 3835.7,223.66 3843.7,\ +213.97 3849.5,204.54", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4020.5,178", + width=1.0652]; + "transcript to gene relationship" -> "object namespace" [color=blue, + label="object namespace", + lp="4064.5,221.5", + pos="e,4012.8,195.76 2770.7,251.75 2790.2,249.85 2810.5,248.14 2829.5,247 2861.5,245.09 3953.9,243.46 3982.5,229 3993,223.7 4001.3,214.03 \ +4007.5,204.59", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4171.5,178", + width=1.0652]; + "transcript to gene relationship" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4224.5,221.5", + pos="e,4163.5,195.78 2770.7,251.72 2790.2,249.82 2810.5,248.12 2829.5,247 2865.6,244.87 4100.1,245.11 4132.5,229 4143.2,223.67 4151.9,\ +213.85 4158.3,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4342.5,178", + width=1.0652]; + "transcript to gene relationship" -> "object label closure" [color=blue, + label="object label closure", + lp="4390,221.5", + pos="e,4334.2,195.8 2770.3,251.74 2789.9,249.82 2810.3,248.11 2829.5,247 2870.3,244.63 4265.7,246.95 4302.5,229 4313.3,223.7 4322.2,213.88 \ +4328.8,204.34", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4504.5,178", + width=2.347]; + "transcript to gene relationship" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4553,221.5", + pos="e,4495.6,196.31 2770.3,251.72 2789.9,249.81 2810.3,248.1 2829.5,247 2874.8,244.39 4422.6,248.64 4463.5,229 4474.3,223.79 4483.3,\ +214.18 4490,204.77", style=solid]; type [height=0.5, - pos="2915.5,178", + pos="4638.5,178", width=0.86659]; "transcript to gene relationship" -> type [color=blue, label=type, - lp="2946.5,221.5", - pos="e,2924.9,195.54 1820.7,251.77 1840.2,249.87 1860.5,248.15 1879.5,247 1908.5,245.24 2904.1,249.7 2924.5,229 2930.7,222.69 2930.6,\ -213.66 2928.3,205", + lp="4652.5,221.5", + pos="e,4639.3,196.18 2770.3,251.7 2789.9,249.79 2810.3,248.09 2829.5,247 2854.4,245.58 4607,244.55 4626.5,229 4633.3,223.54 4636.7,214.93 \ +4638.2,206.37", style=solid]; category [height=0.5, - pos="3016.5,178", + pos="4739.5,178", width=1.4263]; "transcript to gene relationship" -> category [color=blue, label=category, - lp="3021,221.5", - pos="e,3005.1,195.87 1820.7,251.76 1840.2,249.86 1860.5,248.15 1879.5,247 1939.8,243.36 2910.9,252.57 2966.5,229 2979,223.68 2990.1,213.59 \ -2998.6,203.85", + lp="4733,221.5", + pos="e,4723.9,195.25 2770.3,251.7 2789.9,249.79 2810.3,248.09 2829.5,247 2880.6,244.09 4624,245.37 4672.5,229 4688.7,223.53 4704.2,212.51 \ +4716.2,202.2", style=solid]; subject [height=0.5, - pos="3130.5,178", + pos="4853.5,178", width=1.2277]; "transcript to gene relationship" -> subject [color=blue, label=subject, - lp="3113.5,221.5", - pos="e,3113.5,194.75 1820.7,251.74 1840.2,249.84 1860.5,248.14 1879.5,247 1944.8,243.1 2994.1,248.62 3056.5,229 3074.5,223.34 3092.1,\ -211.75 3105.6,201.16", + lp="4829.5,221.5", + pos="e,4834.2,194.33 2770.3,251.69 2789.9,249.78 2810.3,248.09 2829.5,247 2937,240.91 4664.7,257.79 4768.5,229 4789.2,223.25 4810.1,211.09 \ +4826,200.2", style=solid]; object [height=0.5, - pos="3173.5,91", + pos="4896.5,91", width=1.0832]; "transcript to gene relationship" -> object [color=blue, label=object, - lp="3216.5,178", - pos="e,3186.9,108.09 1820.7,251.72 1840.2,249.83 1860.5,248.13 1879.5,247 1949.6,242.85 3077.6,253.21 3143.5,229 3186,213.39 3191.2,186.96 \ -3196.5,142 3197.3,135.38 3198.4,133.39 3196.5,127 3195.5,123.55 3194,120.13 3192.2,116.85", + lp="4940.5,178", + pos="e,4909.9,108.09 2770.3,251.68 2789.9,249.78 2810.3,248.08 2829.5,247 2885.8,243.82 4805.8,246.23 4859.5,229 4883.8,221.2 4892.1,\ +217.1 4906.5,196 4920.4,175.59 4916.6,166.51 4919.5,142 4920.3,135.38 4921.4,133.39 4919.5,127 4918.5,123.55 4917,120.13 4915.2,\ +116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="1926.5,265", + pos="2876.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2057.5,265", + pos="3007.5,265", width=2.0762]; subject -> object [label=relation, - lp="3168.5,134.5", - pos="e,3155.6,107.23 3131.6,159.55 3132.8,149.57 3135.3,137.07 3140.5,127 3142.7,122.68 3145.6,118.52 3148.8,114.66"]; + lp="4891.5,134.5", + pos="e,4878.6,107.23 4854.6,159.55 4855.8,149.57 4858.3,137.07 4863.5,127 4865.7,122.68 4868.6,118.52 4871.8,114.66"]; relation [height=0.5, - pos="3118.5,18", + pos="4841.5,18", width=1.2999]; - subject -> relation [pos="e,3119.8,36.188 3129.2,159.79 3127.1,132.48 3123,78.994 3120.6,46.38", + subject -> relation [pos="e,4842.8,36.188 4852.2,159.79 4850.1,132.48 4846,78.994 4843.6,46.38", style=dotted]; "transcript to gene relationship_subject" [color=blue, height=0.5, label=transcript, - pos="2207.5,265", + pos="3157.5,265", width=1.5887]; - object -> relation [pos="e,3131.3,35.54 3161,73.889 3154.1,64.939 3145.3,53.617 3137.5,43.584", + object -> relation [pos="e,4854.3,35.54 4884,73.889 4877.1,64.939 4868.3,53.617 4860.5,43.584", style=dotted]; "transcript to gene relationship_object" [color=blue, height=0.5, label=gene, - pos="2315.5,265", + pos="3265.5,265", width=0.92075]; } diff --git a/graphviz/transcript_to_gene_relationship.svg b/graphviz/transcript_to_gene_relationship.svg index 5c40843067..b8e3373a35 100644 --- a/graphviz/transcript_to_gene_relationship.svg +++ b/graphviz/transcript_to_gene_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + transcript to gene relationship - -transcript to gene relationship + +transcript to gene relationship @@ -24,9 +24,9 @@ transcript to gene relationship->sequence feature relationship - - -is_a + + +is_a @@ -37,9 +37,9 @@ transcript to gene relationship->id - - -id + + +id @@ -50,9 +50,9 @@ transcript to gene relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ transcript to gene relationship->name - - -name + + +name @@ -76,9 +76,9 @@ transcript to gene relationship->description - - -description + + +description @@ -89,9 +89,9 @@ transcript to gene relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ transcript to gene relationship->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ transcript to gene relationship->negated - - -negated + + +negated @@ -128,9 +128,9 @@ transcript to gene relationship->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ transcript to gene relationship->publications - - -publications + + +publications @@ -154,9 +154,9 @@ transcript to gene relationship->has evidence - - -has evidence + + +has evidence @@ -167,9 +167,9 @@ transcript to gene relationship->knowledge source - - -knowledge source + + +knowledge source @@ -180,9 +180,9 @@ transcript to gene relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -193,9 +193,9 @@ transcript to gene relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -206,9 +206,9 @@ transcript to gene relationship->timepoint - - -timepoint + + +timepoint @@ -219,9 +219,9 @@ transcript to gene relationship->original subject - - -original subject + + +original subject @@ -232,123 +232,266 @@ transcript to gene relationship->original predicate - - -original predicate + + +original predicate original object - -string + +string transcript to gene relationship->original object - - -original object + + +original object - + +subject category + +ontology class + + + +transcript to gene relationship->subject category + + +subject category + + + +object category + +ontology class + + + +transcript to gene relationship->object category + + +object category + + + +subject closure + +string + + + +transcript to gene relationship->subject closure + + +subject closure + + + +object closure + +string + + + +transcript to gene relationship->object closure + + +object closure + + + +subject category closure + +ontology class + + + +transcript to gene relationship->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +transcript to gene relationship->object category closure + + +object category closure + + + +subject namespace + +string + + + +transcript to gene relationship->subject namespace + + +subject namespace + + + +object namespace + +string + + + +transcript to gene relationship->object namespace + + +object namespace + + + +subject label closure + +string + + + +transcript to gene relationship->subject label closure + + +subject label closure + + + +object label closure + +string + + + +transcript to gene relationship->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +transcript to gene relationship->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + transcript to gene relationship->type - - -type + + +type - + category - -category + +category - + transcript to gene relationship->category - - -category + + +category - + subject - -subject + +subject - + transcript to gene relationship->subject - - -subject + + +subject - + object - -object + +object - + transcript to gene relationship->object - - -object + + +object - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + transcript to gene relationship_subject - -transcript + +transcript - + object->relation - - + + - + transcript to gene relationship_object - -gene + +gene diff --git a/graphviz/variant_as_a_model_of_disease_association.gv b/graphviz/variant_as_a_model_of_disease_association.gv index 433d41245f..17afe69b65 100644 --- a/graphviz/variant_as_a_model_of_disease_association.gv +++ b/graphviz/variant_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4369.4,283"]; + graph [bb="0,0,6090.4,283"]; node [label="\N"]; "variant as a model of disease association" [height=0.5, label="variant as a model of disease association", - pos="2531.2,265", + pos="3424.2,265", width=5.5606]; "variant to disease association" [height=0.5, pos="148.19,178", width=4.1163]; "variant as a model of disease association" -> "variant to disease association" [label=is_a, - lp="804.19,221.5", - pos="e,252.43,190.88 2332,263.09 2008.4,260.92 1348.6,253.59 790.19,229 574.34,219.49 520.41,214.97 305.19,196 291.45,194.79 277.05,193.4 \ -262.78,191.94"]; + lp="798.19,221.5", + pos="e,252.43,190.86 3225.1,262.79 2695.2,259.36 1258.8,248.48 784.19,229 570.97,220.25 517.75,214.82 305.19,196 291.45,194.78 277.05,\ +193.39 262.78,191.93"]; "model to disease association mixin" [height=0.5, pos="486.19,178", width=4.7843]; "variant as a model of disease association" -> "model to disease association mixin" [label=uses, - lp="1025.7,221.5", - pos="e,596.2,191.85 2331.3,264 2040.1,262.97 1482.6,257.04 1009.2,229 870.7,220.8 712.16,204.69 606.28,192.97"]; + lp="1015.7,221.5", + pos="e,593.58,192.08 3224.7,263.25 2725.1,261.03 1430,253.06 999.19,229 863.22,221.41 707.62,205.17 603.78,193.25"]; "entity to disease association mixin" [height=0.5, pos="847.19,178", width=4.7482]; "variant as a model of disease association" -> "entity to disease association mixin" [label=uses, - lp="1172.7,221.5", - pos="e,923.01,194.2 2333.2,262.25 2008.9,258.83 1378.3,249.71 1156.2,229 1080.3,221.93 994.88,207.61 933.1,196.1"]; + lp="1170.7,221.5", + pos="e,921.56,194.24 3223.8,264.66 2746.6,265.64 1552.7,264.33 1154.2,229 1078.4,222.28 993.03,207.81 931.59,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "variant as a model of disease association" -> id [color=blue, label=id, - lp="1293.2,221.5", - pos="e,1103.2,190.01 2332.9,262.54 2034.1,259.64 1482.7,251.37 1286.2,229 1212.3,220.59 1193.9,215.79 1122.2,196 1119.1,195.14 1115.9,\ -194.18 1112.7,193.17", + lp="1288.2,221.5", + pos="e,1103.2,189.98 3225,262.89 2730.1,259.82 1470.7,250.02 1281.2,229 1209.5,221.04 1191.7,215.43 1122.2,196 1119.1,195.13 1115.9,194.17 \ +1112.7,193.15", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "variant as a model of disease association" -> iri [color=blue, label=iri, - lp="1411.2,221.5", - pos="e,1207.8,190.16 2334.6,261.58 2060.5,257.58 1577.7,248.04 1403.2,229 1324.5,220.41 1304.9,215.46 1228.2,196 1224.8,195.13 1221.2,\ -194.16 1217.7,193.14", + lp="1401.2,221.5", + pos="e,1208.1,190.19 3225.5,262.61 2749.7,259 1571.6,248.22 1393.2,229 1318.8,220.99 1300.6,214.78 1228.2,196 1224.8,195.12 1221.3,194.16 \ +1217.8,193.14", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "variant as a model of disease association" -> name [color=blue, label=name, - lp="1516.2,221.5", - pos="e,1332.8,191.18 2333.5,262.12 2079.4,258.86 1652.2,250.34 1496.2,229 1442.8,221.7 1383,205.92 1342.4,194.03", + lp="1508.2,221.5", + pos="e,1331.9,191.54 3225,263.04 2765.2,260.45 1656.5,251.88 1488.2,229 1437.4,222.09 1380.8,206.58 1341.9,194.65", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "variant as a model of disease association" -> description [color=blue, label=description, - lp="1635.7,221.5", - pos="e,1479.7,193.95 2332.1,263.12 2100.1,260.95 1731.4,253.58 1595.2,229 1558.7,222.41 1518.9,208.97 1489.4,197.69", + lp="1628.7,221.5", + pos="e,1478,194.15 3224.5,263.74 2782,262.64 1745.5,257.07 1588.2,229 1553.3,222.78 1515.6,209.42 1487.5,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "variant as a model of disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1778.2,221.5", - pos="e,1619.8,192.73 2333.4,261.99 2134.5,258.78 1842.1,250.46 1731.2,229 1695.7,222.14 1657.2,208.11 1629.2,196.66", + lp="1774.2,221.5", + pos="e,1618.8,192.95 3224.4,263.54 2807.3,262.04 1870.6,255.7 1727.2,229 1692.7,222.58 1655.4,208.62 1628.3,197.07", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "variant as a model of disease association" -> negated [color=blue, label=negated, - lp="1927.2,221.5", - pos="e,1740.4,190.33 2333.2,262.24 2207.9,258.87 2042.9,250.25 1898.2,229 1846.6,221.42 1788.8,205.31 1750.3,193.41", + lp="1929.2,221.5", + pos="e,1740,190.46 3224,264.62 2870.6,264.84 2150,261.15 1900.2,229 1847.6,222.23 1788.9,205.81 1750,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "variant as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2057.7,221.5", - pos="e,1888.5,193.28 2338.7,260.05 2243.5,255.74 2127.2,246.91 2024.2,229 1980.9,221.48 1933,207.6 1898,196.37", + lp="2067.7,221.5", + pos="e,1888.9,193.2 3223.7,264.76 2895.4,265.04 2257.4,261.19 2034.2,229 1987.5,222.26 1935.7,207.87 1898.5,196.25", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "variant as a model of disease association" -> publications [color=blue, label=publications, - lp="2191.2,221.5", - pos="e,2037.6,193.32 2352.5,256.85 2287.3,251.85 2213.4,243.37 2147.2,229 2112.7,221.52 2075.1,208.14 2047.1,197.11", + lp="2213.2,221.5", + pos="e,2039.9,192.85 3224,264.89 2922.4,265.12 2366,260.97 2169.2,229 2127.8,222.28 2082.3,207.95 2049.6,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.0943]; "variant as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2330.7,221.5", - pos="e,2192.1,194.37 2399.9,251.41 2362.2,246.18 2321.2,238.93 2284.2,229 2255.8,221.39 2225.2,209.08 2201.5,198.58", + lp="2371.7,221.5", + pos="e,2198.2,193.63 3224.1,263.9 2955.4,262.68 2492.2,256.48 2325.2,229 2284.8,222.35 2240.4,208.52 2207.9,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=3.015]; "variant as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2459.7,221.5", - pos="e,2369.6,196.24 2435.7,249.05 2421.4,244.15 2407.3,237.64 2395.2,229 2386.6,222.9 2379.7,213.84 2374.4,205.1", + lp="2526.7,221.5", + pos="e,2387.7,195.61 3228,261.31 2968.1,257.07 2534,247.34 2462.2,229 2439.1,223.1 2415.1,211.34 2396.4,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "variant as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2627.2,221.5", - pos="e,2552.8,194.65 2527.4,246.59 2526.1,236.37 2526.3,223.63 2532.2,214 2535.4,208.82 2539.6,204.35 2544.4,200.52", + lp="2698.2,221.5", + pos="e,2594.2,196.33 3226.8,261.94 2991.2,258.54 2625.8,249.92 2603.2,229 2597.1,223.32 2594.7,214.91 2594.1,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -143,9 +143,8 @@ digraph { width=3.015]; "variant as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2851.7,221.5", - pos="e,2788.5,194.64 2647.4,250.3 2672.6,245.25 2698.7,238.37 2722.2,229 2733.5,224.48 2734.4,219.64 2745.2,214 2755.9,208.42 2767.7,\ -203.13 2779.1,198.44", + lp="2906.7,221.5", + pos="e,2810.4,195.87 3233,259.58 3055.1,254.5 2815.1,244.77 2800.2,229 2793,221.43 2796.5,212.05 2803.3,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -154,8 +153,8 @@ digraph { width=1.5346]; "variant as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3012.2,221.5", - pos="e,2998.2,195.38 2674.5,252.39 2798.2,242.34 2957.4,229.36 2958.2,229 2965.6,225.82 2979,214.01 2990.8,202.67", + lp="3061.2,221.5", + pos="e,3013.6,196.43 3241.7,257.58 3145.2,252.48 3043.2,243.69 3026.2,229 3019.6,223.36 3016.3,214.85 3014.7,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -164,9 +163,8 @@ digraph { width=1.0652]; "variant as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3129.2,221.5", - pos="e,3105.1,193.27 2671.8,252.17 2695,250.35 2718.7,248.56 2741.2,247 2810,242.22 2985.8,250.9 3051.2,229 3052.5,228.55 3076.2,212.71 \ -3096.6,198.97", + lp="3159.2,221.5", + pos="e,3110.4,194.82 3255.4,255.26 3183.9,249.78 3114.3,241.36 3103.2,229 3096.5,221.56 3099.1,211.86 3104.6,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -175,9 +173,8 @@ digraph { width=1.5887]; "variant as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3269.7,221.5", - pos="e,3224.9,195.47 2669.8,251.98 2693.6,250.15 2718.1,248.4 2741.2,247 2790.6,244 3140.5,247.98 3186.2,229 3193.5,225.96 3206.4,214.16 \ -3217.7,202.78", + lp="3285.7,221.5", + pos="e,3226.4,195.8 3281,252.37 3253.9,247.21 3231.2,239.76 3222.2,229 3216.3,222.05 3217.6,213.06 3221.5,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -186,121 +183,238 @@ digraph { width=1.0652]; "variant as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3399.7,221.5", - pos="e,3352.8,196.31 2668.6,251.87 2692.8,250.02 2717.7,248.3 2741.2,247 2774.2,245.17 3309.4,248.42 3336.2,229 3343.6,223.63 3348,214.91 \ -3350.5,206.25", + lp="3409.7,221.5", + pos="e,3351.6,196.07 3378.2,247.43 3370.4,242.64 3363.2,236.59 3358.2,229 3353.8,222.32 3352,214 3351.6,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3487.2,178", + width=2.1304]; + "variant as a model of disease association" -> "subject category" [color=blue, + label="subject category", + lp="3533.7,221.5", + pos="e,3481.8,196.22 3447.6,247.1 3453.9,241.81 3460.3,235.61 3465.2,229 3470.4,221.97 3474.7,213.49 3478.1,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3658.2,178", + width=2.1304]; + "variant as a model of disease association" -> "object category" [color=blue, + label="object category", + lp="3676.7,221.5", + pos="e,3642.1,195.91 3534.8,249.98 3556.1,244.98 3577.8,238.2 3597.2,229 3610.8,222.54 3624,212.41 3634.6,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3791.2,178", + width=1.0652]; + "variant as a model of disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3813.7,221.5", + pos="e,3778.1,195.42 3565.2,252.18 3640.2,245.18 3720.1,236.29 3736.2,229 3749.4,223.04 3761.5,212.72 3771.1,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3890.2,178", + width=1.0652]; + "variant as a model of disease association" -> "object closure" [color=blue, + label="object closure", + lp="3934.2,221.5", + pos="e,3888.7,196.16 3566.8,252.35 3589.3,250.54 3612.4,248.71 3634.2,247 3660.6,244.93 3851.1,245.06 3872.2,229 3879.5,223.46 3883.8,\ +214.71 3886.4,206.06", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4023.2,178", + width=2.1304]; + "variant as a model of disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4092.7,221.5", + pos="e,4016.1,196.07 3563.9,252.1 3587.4,250.27 3611.5,248.5 3634.2,247 3673.5,244.41 3953.7,248.07 3988.2,229 3997.9,223.61 4005.6,214.23 \ +4011.2,205.04", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4216.2,178", + width=2.1304]; + "variant as a model of disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4283.7,221.5", + pos="e,4210.2,196.1 3561.9,251.9 3586,250.05 3610.8,248.33 3634.2,247 3664.7,245.27 4157.6,244.11 4184.2,229 4193.6,223.65 4200.7,214.28 \ +4205.7,205.08", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4406.2,178", + width=1.0652]; + "variant as a model of disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4456.2,221.5", + pos="e,4399.2,196.18 3560.8,251.82 3585.2,249.96 3610.4,248.25 3634.2,247 3675.1,244.85 4335.1,248.36 4371.2,229 4381,223.74 4388.6,214.39 \ +4394.3,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4565.2,178", + width=1.0652]; + "variant as a model of disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4609.2,221.5", + pos="e,4557.8,195.73 3560.2,251.78 3584.8,249.91 3610.3,248.21 3634.2,247 3683.8,244.49 4484.1,251.8 4528.2,229 4538.5,223.67 4546.7,\ +213.98 4552.7,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4716.2,178", + width=1.0652]; + "variant as a model of disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4769.2,221.5", + pos="e,4708.2,195.76 3559.9,251.74 3584.6,249.87 3610.2,248.18 3634.2,247 3692.1,244.16 4625.3,254.87 4677.2,229 4687.9,223.66 4696.5,\ +213.83 4702.9,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4887.2,178", + width=1.0652]; + "variant as a model of disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4934.7,221.5", + pos="e,4878.9,195.78 3559.7,251.71 3584.4,249.84 3610.1,248.15 3634.2,247 3667.8,245.39 4816.9,243.82 4847.2,229 4858,223.68 4866.9,213.87 \ +4873.5,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5029.2,178", + width=2.347]; + "variant as a model of disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5090.7,221.5", + pos="e,5026.8,196.45 3559.4,251.7 3584.2,249.82 3610,248.14 3634.2,247 3672.3,245.21 4976.5,250.34 5008.2,229 5016,223.72 5020.9,214.91 \ +5024,206.14", style=solid]; type [height=0.5, - pos="3442.2,178", + pos="5163.2,178", width=0.86659]; "variant as a model of disease association" -> type [color=blue, label=type, - lp="3476.2,221.5", - pos="e,3453.2,194.96 2667.8,251.83 2692.2,249.98 2717.4,248.26 2741.2,247 2761,245.95 3441.3,243.2 3455.2,229 3461.6,222.4 3460.8,213.03 \ -3457.5,204.19", + lp="5187.2,221.5", + pos="e,5169.1,196.12 3559.1,251.69 3584,249.81 3609.9,248.13 3634.2,247 3655.4,246.02 5149.2,244.12 5164.2,229 5170.1,223.03 5171.4,214.44 \ +5170.7,206.05", style=solid]; category [height=0.5, - pos="3543.2,178", + pos="5264.2,178", width=1.4263]; "variant as a model of disease association" -> category [color=blue, label=category, - lp="3549.7,221.5", - pos="e,3532.7,195.81 2667.8,251.81 2692.2,249.95 2717.4,248.24 2741.2,247 2783.1,244.81 3457.9,246.11 3496.2,229 3508.3,223.61 3518.7,\ -213.5 3526.6,203.78", + lp="5263.7,221.5", + pos="e,5251.2,195.44 3559.1,251.69 3584,249.81 3609.9,248.12 3634.2,247 3677.8,244.99 5166.4,244.63 5207.2,229 5221.3,223.6 5234.2,212.99 \ +5244.2,202.93", style=solid]; predicate [height=0.5, - pos="3667.2,178", + pos="5388.2,178", width=1.5165]; "variant as a model of disease association" -> predicate [color=blue, label=predicate, - lp="3653.2,221.5", - pos="e,3647.7,194.98 2667.5,251.78 2692,249.92 2717.4,248.22 2741.2,247 2834.9,242.21 3495.2,255.32 3585.2,229 3604.7,223.29 3624.3,211.66 \ -3639.4,201.05", + lp="5370.2,221.5", + pos="e,5367.2,194.81 3559.1,251.68 3584,249.8 3609.9,248.11 3634.2,247 3726.6,242.77 5209.8,252.9 5299.2,229 5320.4,223.32 5342,211.41 \ +5358.5,200.63", style=solid]; object [height=0.5, - pos="4254.2,91", + pos="5975.2,91", width=1.0832]; "variant as a model of disease association" -> object [color=blue, label=object, - lp="3789.2,178", - pos="e,4215.5,94.237 2667.2,251.75 2691.8,249.89 2717.3,248.19 2741.2,247 2793.9,244.37 3641.7,247.32 3691.2,229 3712.8,221 3714.1,211.5 \ -3731.2,196 3747.9,180.78 3746.9,170.09 3767.2,160 3843.5,121.97 4097.5,101.88 4205.2,94.891", + lp="5510.2,178", + pos="e,5936.5,94.237 3559.1,251.66 3584,249.78 3609.9,248.11 3634.2,247 3683.4,244.76 5361.5,244.82 5408.2,229 5431.3,221.15 5433.7,212.02 \ +5452.2,196 5469.3,181.17 5467.9,170.09 5488.2,160 5564.5,121.97 5818.5,101.88 5926.2,94.891", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3905.2,178", + pos="5626.2,178", width=2.3651]; "variant as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3893.2,221.5", - pos="e,3872.8,194.78 2666.9,251.74 2691.6,249.88 2717.2,248.18 2741.2,247 2855.6,241.37 3659.6,250.47 3772.2,229 3803.8,222.97 3837.7,\ -210.12 3863.3,198.96", + lp="5614.2,221.5", + pos="e,5594,194.73 3558.8,251.67 3583.8,249.79 3609.8,248.1 3634.2,247 3737.4,242.33 5391.7,247.96 5493.2,229 5524.9,223.08 5558.9,210.15 \ +5584.6,198.93", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4084.2,178", + pos="5805.2,178", width=2.1123]; "variant as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4074.2,221.5", - pos="e,4055.4,194.81 2666.7,251.71 2691.4,249.84 2717.1,248.15 2741.2,247 2877,240.51 3832.1,256.85 3965.2,229 3993.5,223.07 4023.6,210.39 \ -4046.4,199.28", + lp="5795.2,221.5", + pos="e,5776.4,194.86 3558.8,251.66 3583.8,249.77 3609.8,248.09 3634.2,247 3748.1,241.9 5574.5,252.01 5686.2,229 5714.5,223.16 5744.6,\ +210.47 5767.4,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4214.2,178", + pos="5935.2,178", width=1.011]; "variant as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4221.7,221.5", - pos="e,4197.5,194.29 2666.4,251.7 2691.2,249.82 2717,248.13 2741.2,247 2818.8,243.36 4065,251.99 4139.2,229 4157.6,223.29 4175.7,211.46 \ -4189.5,200.75", + lp="5942.7,221.5", + pos="e,5918.8,194.07 3558.8,251.64 3583.8,249.76 3609.8,248.08 3634.2,247 3696,244.25 5801.1,247.16 5860.2,229 5878.8,223.29 5897,211.35 \ +5910.8,200.57", style=solid]; subject [height=0.5, - pos="4325.2,178", + pos="6046.2,178", width=1.2277]; "variant as a model of disease association" -> subject [color=blue, label=subject, - lp="4324.2,221.5", - pos="e,4314.4,195.87 2666.1,251.69 2691,249.81 2716.9,248.12 2741.2,247 2783.8,245.03 4238,245.96 4277.2,229 4289.4,223.69 4300.1,213.6 \ -4308.2,203.86", + lp="6045.2,221.5", + pos="e,6035.4,195.89 3558.5,251.65 3583.7,249.76 3609.7,248.08 3634.2,247 3699.8,244.1 5937.9,254.98 5998.2,229 6010.4,223.72 6021.1,\ +213.63 6029.2,203.88", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2788.2,265", + pos="3681.2,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2919.2,265", + pos="3812.2,265", width=2.0762]; "variant to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3090.2,265", + pos="3983.2,265", width=2.1665]; relation [height=0.5, - pos="4289.2,18", + pos="6010.2,18", width=1.2999]; - object -> relation [pos="e,4280.7,36.198 4262.5,73.174 4266.6,64.896 4271.6,54.723 4276.2,45.438", + object -> relation [pos="e,6001.7,36.198 5983.5,73.174 5987.6,64.896 5992.6,54.723 5997.2,45.438", style=dotted]; "variant to disease association_object" [color=blue, height=0.5, label="named thing", - pos="3256.2,265", + pos="4149.2,265", width=1.9318]; subject -> object [label=relation, - lp="4283.2,134.5", - pos="e,4250.4,109.01 4288.8,167.42 4276,162.12 4262.8,154.06 4255.2,142 4250.9,135.26 4249.6,126.93 4249.6,119.01"]; - subject -> relation [pos="e,4293.4,36.005 4321.5,160.05 4317.1,139.44 4309.3,103.63 4302.2,73 4300.2,64.183 4297.9,54.574 4295.8,45.938", + lp="6004.2,134.5", + pos="e,5971.4,109.01 6009.8,167.42 5997,162.12 5983.8,154.06 5976.2,142 5971.9,135.26 5970.6,126.93 5970.6,119.01"]; + subject -> relation [pos="e,6014.4,36.005 6042.5,160.05 6038.1,139.44 6030.3,103.63 6023.2,73 6021.2,64.183 6018.9,54.574 6016.8,45.938", style=dotted]; "variant as a model of disease association_subject" [color=blue, height=0.5, label="sequence variant", - pos="3434.2,265", + pos="4327.2,265", width=2.5095]; } diff --git a/graphviz/variant_as_a_model_of_disease_association.svg b/graphviz/variant_as_a_model_of_disease_association.svg index 2d44d94793..b6676f6881 100644 --- a/graphviz/variant_as_a_model_of_disease_association.svg +++ b/graphviz/variant_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant as a model of disease association - -variant as a model of disease association + +variant as a model of disease association @@ -24,9 +24,9 @@ variant as a model of disease association->variant to disease association - - -is_a + + +is_a @@ -37,9 +37,9 @@ variant as a model of disease association->model to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant as a model of disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ variant as a model of disease association->id - - -id + + +id @@ -76,9 +76,9 @@ variant as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ variant as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ variant as a model of disease association->description - - -description + + +description @@ -115,9 +115,9 @@ variant as a model of disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ variant as a model of disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant as a model of disease association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ variant as a model of disease association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ variant as a model of disease association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ variant as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ variant as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ variant as a model of disease association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ variant as a model of disease association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ variant as a model of disease association->original predicate - - -original predicate + + +original predicate @@ -258,168 +258,311 @@ variant as a model of disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +variant as a model of disease association->subject category + + +subject category + + + +object category + +ontology class + + + +variant as a model of disease association->object category + + +object category + + + +subject closure + +string + + + +variant as a model of disease association->subject closure + + +subject closure + + + +object closure + +string + + + +variant as a model of disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +variant as a model of disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +variant as a model of disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +variant as a model of disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +variant as a model of disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +variant as a model of disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +variant as a model of disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +variant as a model of disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + variant as a model of disease association->type - - -type + + +type - + category - -category + +category - + variant as a model of disease association->category - - -category + + +category - + predicate - -predicate + +predicate - + variant as a model of disease association->predicate - - -predicate + + +predicate - + object - -object + +object - + variant as a model of disease association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + variant as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + variant as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + variant as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + subject - -subject + +subject - + variant as a model of disease association->subject - - -subject + + +subject - + association_type - -string + +string - + association_category - -category type + +category type - + variant to disease association_predicate - -predicate type + +predicate type - + relation - -relation + +relation - + object->relation - - + + - + variant to disease association_object - -named thing + +named thing - + subject->object - - -relation + + +relation - + subject->relation - - + + - + variant as a model of disease association_subject - -sequence variant + +sequence variant diff --git a/graphviz/variant_to_disease_association.gv b/graphviz/variant_to_disease_association.gv index 6d3869c782..71a6595ce9 100644 --- a/graphviz/variant_to_disease_association.gv +++ b/graphviz/variant_to_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4206.4,283"]; + graph [bb="0,0,5927.4,283"]; node [label="\N"]; "variant to disease association" [height=0.5, label="variant to disease association", - pos="2355.4,265", + pos="3248.4,265", width=4.1163]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to disease association" -> association [label=is_a, - lp="629.39,221.5", - pos="e,106.48,190.76 2207.5,263.43 1907.3,261.74 1204.8,255.09 615.39,229 400.88,219.5 345.65,228.45 133.39,196 127.91,195.16 122.23,\ + lp="623.39,221.5", + pos="e,106.48,190.75 3100.7,263.13 2619.6,260.13 1100.1,249.25 609.39,229 397.51,220.26 343.01,228.13 133.39,196 127.91,195.16 122.23,\ 194.11 116.58,192.95"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to disease association" -> "variant to entity association mixin" [label=uses, - lp="849.89,221.5", - pos="e,421.48,191.8 2207.3,264.16 1935,263.67 1336.7,258.9 833.39,229 695.22,220.79 537,204.65 431.52,192.92"]; + lp="839.89,221.5", + pos="e,418.88,192.02 3100.4,263.48 2645.3,261.62 1269.9,254.03 823.39,229 687.74,221.4 532.47,205.12 429.03,193.2"]; "entity to disease association mixin" [height=0.5, pos="671.39,178", width=4.7482]; "variant to disease association" -> "entity to disease association mixin" [label=uses, - lp="996.89,221.5", - pos="e,747.22,194.2 2208.1,262.77 1903.9,259.8 1214.8,250.85 980.39,229 904.54,221.93 819.09,207.61 757.31,196.1"]; + lp="994.89,221.5", + pos="e,745.77,194.24 3100.3,264.54 2664.6,265.69 1392.3,265.7 978.39,229 902.6,222.28 817.24,207.81 755.8,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "variant to disease association" -> id [color=blue, label=id, - lp="1117.4,221.5", - pos="e,927.37,190.01 2208.1,263.01 1925.9,260.58 1318.7,252.71 1110.4,229 1036.5,220.59 1018.1,215.79 946.39,196 943.28,195.14 940.08,\ -194.18 936.89,193.17", + lp="1112.4,221.5", + pos="e,927.38,189.98 3100.8,263.2 2648.8,260.52 1301.9,250.8 1105.4,229 1033.7,221.04 1015.9,215.43 946.39,196 943.29,195.13 940.09,194.17 \ +936.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "variant to disease association" -> iri [color=blue, label=iri, - lp="1235.4,221.5", - pos="e,1032,190.16 2208.9,262.29 1948,258.76 1413.1,249.27 1227.4,229 1148.7,220.41 1129.1,215.46 1052.4,196 1049,195.13 1045.4,194.16 \ -1041.9,193.14", + lp="1225.4,221.5", + pos="e,1032.3,190.19 3100.9,262.99 2665.1,259.81 1402.6,248.95 1217.4,229 1143,220.99 1124.8,214.78 1052.4,196 1049,195.12 1045.5,194.16 \ +1042.1,193.14", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "variant to disease association" -> name [color=blue, label=name, - lp="1340.4,221.5", - pos="e,1157,191.18 2208.1,262.72 1964.3,259.99 1487.3,251.82 1320.4,229 1267,221.7 1207.2,205.92 1166.6,194.03", + lp="1332.4,221.5", + pos="e,1156.2,191.54 3100.6,263.32 2678.7,261.1 1487.3,252.79 1312.4,229 1261.6,222.09 1205,206.58 1166.1,194.65", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "variant to disease association" -> description [color=blue, label=description, - lp="1459.9,221.5", - pos="e,1304,193.95 2207.6,263.54 1982.9,261.98 1566.1,255.48 1419.4,229 1382.9,222.41 1343.1,208.97 1313.6,197.69", + lp="1452.9,221.5", + pos="e,1302.2,194.15 3100.2,263.85 2693,263.06 1576.1,258.23 1412.4,229 1377.6,222.78 1339.8,209.42 1311.7,198.07", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "variant to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1602.4,221.5", - pos="e,1444,192.73 2208.4,262.74 2012.4,260.16 1676.2,252.37 1555.4,229 1519.9,222.14 1481.4,208.11 1453.4,196.66", + lp="1598.4,221.5", + pos="e,1443,192.95 3100.4,263.71 2715.3,262.55 1701.1,256.88 1551.4,229 1516.9,222.58 1479.6,208.62 1452.5,197.07", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "variant to disease association" -> negated [color=blue, label=negated, - lp="1751.4,221.5", - pos="e,1564.6,190.33 2207.5,263.38 2078.8,261.04 1887.4,253.23 1722.4,229 1670.8,221.42 1613,205.31 1574.5,193.41", + lp="1753.4,221.5", + pos="e,1564.2,190.46 3100.1,264.56 2770.9,265.15 1987.1,262.82 1724.4,229 1671.8,222.23 1613.1,205.81 1574.2,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "variant to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1881.9,221.5", - pos="e,1712.7,193.28 2209.4,261.88 2107.6,258.47 1968.9,249.95 1848.4,229 1805.1,221.48 1757.2,207.6 1722.2,196.37", + lp="1891.9,221.5", + pos="e,1713.1,193.2 3100.2,264.68 2792.7,265.38 2094.2,263 1858.4,229 1811.7,222.26 1759.9,207.87 1722.7,196.25", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "variant to disease association" -> publications [color=blue, label=publications, - lp="2015.4,221.5", - pos="e,1861.8,193.32 2214.2,259.42 2141,254.97 2050.7,246.21 1971.4,229 1936.9,221.52 1899.3,208.14 1871.3,197.11", + lp="2037.4,221.5", + pos="e,1864.1,192.85 3100.2,264.8 2815.6,265.52 2202.2,262.92 1993.4,229 1952,222.28 1906.6,207.95 1873.8,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.0943]; "variant to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2154.9,221.5", - pos="e,2016.3,194.37 2240.5,253.59 2198.5,248.25 2150.9,240.39 2108.4,229 2080,221.39 2049.4,209.08 2025.7,198.58", + lp="2195.9,221.5", + pos="e,2022.4,193.63 3100.3,264.08 2844,263.43 2327.8,258.35 2149.4,229 2109,222.35 2064.6,208.52 2032.1,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=3.015]; "variant to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2283.9,221.5", - pos="e,2193.8,196.24 2264.9,250.67 2248.8,245.61 2232.9,238.63 2219.4,229 2210.8,222.9 2203.9,213.84 2198.6,205.1", + lp="2350.9,221.5", + pos="e,2211.9,195.61 3101.9,262.09 2852.1,258.33 2363,248.56 2286.4,229 2263.3,223.1 2239.3,211.34 2220.6,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -133,8 +133,8 @@ digraph { width=3.015]; "variant to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2451.4,221.5", - pos="e,2377,194.65 2351.6,246.59 2350.3,236.37 2350.5,223.63 2356.4,214 2359.6,208.82 2363.8,204.35 2368.6,200.52", + lp="2522.4,221.5", + pos="e,2418.4,196.33 3101.4,262.61 2871.8,259.76 2451.7,251.48 2427.4,229 2421.3,223.32 2418.9,214.91 2418.3,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -143,9 +143,8 @@ digraph { width=3.015]; "variant to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2675.9,221.5", - pos="e,2612.7,194.64 2461.1,252.32 2489.4,247.13 2519.6,239.68 2546.4,229 2557.7,224.48 2558.6,219.64 2569.4,214 2580.1,208.42 2591.9,\ -203.13 2603.3,198.44", + lp="2730.9,221.5", + pos="e,2634.6,195.87 3103.9,260.85 2924.7,256.21 2640.7,246.2 2624.4,229 2617.2,221.43 2620.7,212.05 2627.6,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -154,9 +153,8 @@ digraph { width=1.5346]; "variant to disease association" -> timepoint [color=blue, label=timepoint, - lp="2838.4,221.5", - pos="e,2822.4,195.41 2459.9,252.16 2477.7,250.31 2496.1,248.51 2513.4,247 2573.1,241.79 2727.2,252.21 2782.4,229 2789.8,225.87 2803.2,\ -214.07 2815,202.71", + lp="2885.4,221.5", + pos="e,2837.8,196.43 3107.1,259.56 3000.7,254.9 2869.9,245.81 2850.4,229 2843.9,223.36 2840.5,214.85 2839,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -165,9 +163,8 @@ digraph { width=1.0652]; "variant to disease association" -> "original subject" [color=blue, label="original subject", - lp="2953.4,221.5", - pos="e,2929.3,193.27 2458.6,252.03 2476.8,250.17 2495.7,248.39 2513.4,247 2593.7,240.69 2798.9,254.25 2875.4,229 2876.7,228.56 2900.4,\ -212.71 2920.8,198.98", + lp="2983.4,221.5", + pos="e,2934.6,194.82 3113.1,257.61 3031.2,252.31 2940.2,243.29 2927.4,229 2920.7,221.56 2923.3,211.86 2928.8,202.98", style=solid]; "original predicate" [color=blue, height=0.5, @@ -176,9 +173,8 @@ digraph { width=1.5887]; "variant to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3093.9,221.5", - pos="e,3049.1,195.48 2457.7,251.92 2476.2,250.04 2495.4,248.29 2513.4,247 2568.5,243.04 2959.3,250.09 3010.4,229 3017.7,225.98 3030.6,\ -214.18 3041.9,202.8", + lp="3109.9,221.5", + pos="e,3050.6,195.8 3122.9,255.35 3088.4,250.22 3057.4,242.04 3046.4,229 3040.5,222.05 3041.9,213.06 3045.7,204.62", style=solid]; "original object" [color=blue, height=0.5, @@ -187,121 +183,238 @@ digraph { width=1.0652]; "variant to disease association" -> "original object" [color=blue, label="original object", - lp="3223.9,221.5", - pos="e,3177,196.32 2456.9,251.88 2475.6,249.98 2495.1,248.24 2513.4,247 2549.3,244.57 3131.3,250.08 3160.4,229 3167.8,223.63 3172.2,214.92 \ -3174.8,206.26", + lp="3233.9,221.5", + pos="e,3175.9,196.07 3203.1,247.84 3195,242.99 3187.5,236.8 3182.4,229 3178,222.32 3176.2,214 3175.8,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3311.4,178", + width=2.1304]; + "variant to disease association" -> "subject category" [color=blue, + label="subject category", + lp="3357.9,221.5", + pos="e,3306,196.22 3271.8,247.1 3278.1,241.81 3284.5,235.61 3289.4,229 3294.6,221.97 3298.9,213.49 3302.3,205.54", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3482.4,178", + width=2.1304]; + "variant to disease association" -> "object category" [color=blue, + label="object category", + lp="3500.9,221.5", + pos="e,3466.3,195.91 3350.3,251.92 3374.4,246.78 3399.4,239.45 3421.4,229 3435,222.54 3448.2,212.41 3458.8,202.94", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3615.4,178", + width=1.0652]; + "variant to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3637.9,221.5", + pos="e,3602.3,195.42 3355.1,252.42 3444.5,242.65 3558,230.09 3560.4,229 3573.6,223.04 3585.7,212.72 3595.3,203", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3714.4,178", + width=1.0652]; + "variant to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3758.4,221.5", + pos="e,3712.9,196.21 3352.4,252.13 3370.4,250.27 3388.9,248.48 3406.4,247 3438.6,244.27 3670.6,248.37 3696.4,229 3703.7,223.51 3708.1,\ +214.77 3710.6,206.12", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3847.4,178", + width=2.1304]; + "variant to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3916.9,221.5", + pos="e,3840.4,196.1 3351.1,252 3369.5,250.12 3388.5,248.36 3406.4,247 3451.4,243.58 3772.8,250.74 3812.4,229 3822.1,223.64 3829.8,214.27 \ +3835.4,205.08", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4040.4,178", + width=2.1304]; + "variant to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4107.9,221.5", + pos="e,4034.4,196.11 3350.3,251.87 3368.9,249.98 3388.2,248.25 3406.4,247 3439.8,244.71 3979.3,245.5 4008.4,229 4017.8,223.66 4024.9,\ +214.29 4030,205.1", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4230.4,178", + width=1.0652]; + "variant to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4280.4,221.5", + pos="e,4223.4,196.18 3349.9,251.8 3368.6,249.91 3388.1,248.19 3406.4,247 3450.1,244.15 4156.7,249.69 4195.4,229 4205.2,223.75 4212.9,\ +214.39 4218.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4389.4,178", + width=1.0652]; + "variant to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4433.4,221.5", + pos="e,4382,195.73 3349.4,251.79 3368.3,249.89 3387.9,248.17 3406.4,247 3458.9,243.69 4305.7,253.1 4352.4,229 4362.7,223.67 4370.9,213.99 \ +4376.9,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4540.4,178", + width=1.0652]; + "variant to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4593.4,221.5", + pos="e,4532.4,195.77 3349.4,251.75 3368.3,249.85 3387.9,248.14 3406.4,247 3467.1,243.24 4446.9,256.14 4501.4,229 4512.1,223.66 4520.8,\ +213.84 4527.2,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4711.4,178", + width=1.0652]; + "variant to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4758.9,221.5", + pos="e,4703.1,195.79 3349,251.76 3368,249.85 3387.8,248.13 3406.4,247 3441.5,244.87 4639.8,244.45 4671.4,229 4682.2,223.69 4691.1,213.87 \ +4697.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4853.4,178", + width=2.347]; + "variant to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4914.9,221.5", + pos="e,4851,196.45 3349,251.74 3368,249.82 3387.8,248.11 3406.4,247 3445.9,244.63 4799.5,251.14 4832.4,229 4840.2,223.73 4845.1,214.91 \ +4848.2,206.14", style=solid]; type [height=0.5, - pos="3266.4,178", + pos="4987.4,178", width=0.86659]; "variant to disease association" -> type [color=blue, label=type, - lp="3300.4,221.5", - pos="e,3277.4,194.96 2456.9,251.81 2475.6,249.92 2495.1,248.2 2513.4,247 2534.6,245.61 3264.5,244.23 3279.4,229 3285.8,222.4 3285,213.04 \ -3281.7,204.2", + lp="5011.4,221.5", + pos="e,4993.3,196.12 3349,251.72 3368,249.81 3387.8,248.1 3406.4,247 3428.3,245.7 4972.9,244.63 4988.4,229 4994.3,223.03 4995.6,214.44 \ +4994.9,206.05", style=solid]; category [height=0.5, - pos="3367.4,178", + pos="5088.4,178", width=1.4263]; "variant to disease association" -> category [color=blue, label=category, - lp="3373.9,221.5", - pos="e,3356.9,195.82 2456.9,251.8 2475.6,249.9 2495.1,248.19 2513.4,247 2558.1,244.1 3279.4,247.26 3320.4,229 3332.5,223.62 3342.9,213.51 \ -3350.9,203.79", + lp="5087.9,221.5", + pos="e,5075.4,195.45 3349,251.71 3368,249.8 3387.8,248.1 3406.4,247 3451.5,244.33 4989.2,245.14 5031.4,229 5045.5,223.6 5058.4,213 5068.4,\ +202.94", style=solid]; subject [height=0.5, - pos="3481.4,178", + pos="5202.4,178", width=1.2277]; "variant to disease association" -> subject [color=blue, label=subject, - lp="3465.4,221.5", - pos="e,3464.9,194.72 2456.4,251.81 2475.3,249.9 2494.9,248.18 2513.4,247 2563.1,243.83 3362,244.36 3409.4,229 3426.9,223.34 3443.8,211.92 \ -3456.9,201.42", + lp="5182.4,221.5", + pos="e,5184.4,194.55 3349,251.7 3368,249.79 3387.8,248.09 3406.4,247 3501.6,241.39 5031.9,256.04 5123.4,229 5142.7,223.31 5161.7,211.44 \ +5176.3,200.69", style=solid]; predicate [height=0.5, - pos="3598.4,178", + pos="5319.4,178", width=1.5165]; "variant to disease association" -> predicate [color=blue, label=predicate, - lp="3571.4,221.5", - pos="e,3574.5,194.29 2456.4,251.78 2475.3,249.88 2494.9,248.16 2513.4,247 2622.3,240.16 3389.3,254.42 3495.4,229 3520.3,223.04 3546.1,\ -210.45 3565.7,199.39", + lp="5289.4,221.5", + pos="e,5295,194.11 3349,251.7 3368,249.79 3387.8,248.09 3406.4,247 3506.6,241.13 5114.6,251.24 5212.4,229 5238.4,223.09 5265.6,210.27 \ +5286.1,199.1", style=solid]; object [height=0.5, - pos="3548.4,91", + pos="5269.4,91", width=1.0832]; "variant to disease association" -> object [color=blue, label=object, - lp="3690.4,178", - pos="e,3580.5,101.28 2456.4,251.75 2475.3,249.85 2494.9,248.14 2513.4,247 2574.2,243.24 3551,246.22 3609.4,229 3646.5,218.07 3681.5,193.63 \ -3662.4,160 3647,132.81 3615.9,115.34 3590,104.93", + lp="5411.4,178", + pos="e,5299.2,102.71 3348.6,251.73 3367.7,249.8 3387.7,248.09 3406.4,247 3512.9,240.78 5224.6,257.56 5327.4,229 5355.2,221.27 5369.1,\ +221.08 5383.4,196 5405.7,156.94 5349.7,124.38 5308.5,106.59", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3836.4,178", + pos="5557.4,178", width=2.3651]; "variant to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3824.4,221.5", - pos="e,3804.2,194.68 2456,251.77 2475,249.86 2494.8,248.14 2513.4,247 2645.4,238.92 3573.5,253.63 3703.4,229 3735.1,222.99 3769.1,210.07 \ -3794.8,198.87", + lp="5545.4,221.5", + pos="e,5525.2,194.74 3348.6,251.72 3367.7,249.8 3387.7,248.09 3406.4,247 3518.3,240.5 5314.2,249.54 5424.4,229 5456.1,223.09 5490.1,210.17 \ +5515.8,198.94", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4015.4,178", + pos="5736.4,178", width=2.1123]; "variant to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4005.4,221.5", - pos="e,3986.6,194.82 2456,251.74 2475,249.83 2494.8,248.12 2513.4,247 2666.8,237.77 3745.9,260.34 3896.4,229 3924.7,223.1 3954.8,210.42 \ -3977.6,199.3", + lp="5726.4,221.5", + pos="e,5707.6,194.86 3348.6,251.71 3367.7,249.79 3387.7,248.08 3406.4,247 3529,239.92 5497.1,253.76 5617.4,229 5645.8,223.16 5675.8,210.48 \ +5698.6,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4152.4,178", + pos="5873.4,178", width=1.011]; "variant to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4154.9,221.5", - pos="e,4134.5,193.83 2456,251.72 2475,249.81 2494.8,248.1 2513.4,247 2599.7,241.87 3987.2,252.87 4070.4,229 4090.6,223.19 4110.8,210.96 \ -4126.1,200.04", + lp="5875.9,221.5", + pos="e,5855.5,193.85 3348.6,251.7 3367.7,249.78 3387.7,248.08 3406.4,247 3472.5,243.2 5727.7,247.15 5791.4,229 5811.6,223.23 5831.9,211 \ +5847.1,200.07", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2560.4,265", + pos="3453.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2691.4,265", + pos="3584.4,265", width=2.0762]; subject -> object [label=relation, - lp="3547.4,134.5", - pos="e,3535.7,108.05 3494.3,160.61 3504.3,147.95 3518.3,130.24 3529.5,115.98"]; + lp="5268.4,134.5", + pos="e,5256.7,108.05 5215.3,160.61 5225.3,147.95 5239.3,130.24 5250.5,115.98"]; relation [height=0.5, - pos="3493.4,18", + pos="5214.4,18", width=1.2999]; - subject -> relation [pos="e,3492.1,36.188 3482.7,159.79 3484.8,132.48 3488.8,78.994 3491.3,46.38", + subject -> relation [pos="e,5213.1,36.188 5203.7,159.79 5205.8,132.48 5209.8,78.994 5212.3,46.38", style=dotted]; "variant to disease association_subject" [color=blue, height=0.5, label="named thing", - pos="2853.4,265", + pos="3746.4,265", width=1.9318]; "variant to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3019.4,265", + pos="3912.4,265", width=2.1665]; - object -> relation [pos="e,3506.2,35.54 3535.9,73.889 3529,64.939 3520.2,53.617 3512.4,43.584", + object -> relation [pos="e,5227.2,35.54 5256.9,73.889 5250,64.939 5241.2,53.617 5233.4,43.584", style=dotted]; "variant to disease association_object" [color=blue, height=0.5, label="named thing", - pos="3185.4,265", + pos="4078.4,265", width=1.9318]; } diff --git a/graphviz/variant_to_disease_association.svg b/graphviz/variant_to_disease_association.svg index 38e38426e9..b93071afbc 100644 --- a/graphviz/variant_to_disease_association.svg +++ b/graphviz/variant_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to disease association - -variant to disease association + +variant to disease association @@ -24,9 +24,9 @@ variant to disease association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ variant to disease association->variant to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ variant to disease association->id - - -id + + +id @@ -76,9 +76,9 @@ variant to disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ variant to disease association->name - - -name + + +name @@ -102,9 +102,9 @@ variant to disease association->description - - -description + + +description @@ -115,9 +115,9 @@ variant to disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ variant to disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant to disease association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ variant to disease association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ variant to disease association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ variant to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ variant to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ variant to disease association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ variant to disease association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ variant to disease association->original predicate - - -original predicate + + +original predicate @@ -258,168 +258,311 @@ variant to disease association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +variant to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +variant to disease association->object category + + +object category + + + +subject closure + +string + + + +variant to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +variant to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +variant to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +variant to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +variant to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +variant to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +variant to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +variant to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +variant to disease association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + variant to disease association->type - - -type + + +type - + category - -category + +category - + variant to disease association->category - - -category + + +category - + subject - -subject + +subject - + variant to disease association->subject - - -subject + + +subject - + predicate - -predicate + +predicate - + variant to disease association->predicate - - -predicate + + +predicate - + object - -object + +object - + variant to disease association->object - - -object + + +object - + frequency qualifier - -frequency value + +frequency value - + variant to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + variant to disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + variant to disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + variant to disease association_subject - -named thing + +named thing - + variant to disease association_predicate - -predicate type + +predicate type - + object->relation - - + + - + variant to disease association_object - -named thing + +named thing diff --git a/graphviz/variant_to_gene_association.gv b/graphviz/variant_to_gene_association.gv index 5bb2a54c3f..753f64de4e 100644 --- a/graphviz/variant_to_gene_association.gv +++ b/graphviz/variant_to_gene_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,3423,283"]; + graph [bb="0,0,5151,283"]; node [label="\N"]; "variant to gene association" [height=0.5, label="variant to gene association", - pos="1781.4,265", + pos="2760.4,265", width=3.7733]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to gene association" -> association [label=is_a, - lp="493.39,221.5", - pos="e,106.89,190.66 1645.8,263.4 1409,261.67 904.56,254.96 479.39,229 325.21,219.59 285.77,221.38 133.39,196 128,195.1 122.41,194.02 \ -116.84,192.85"]; + lp="483.39,221.5", + pos="e,106.9,190.64 2624.7,263.4 2199,261.29 892.61,252.97 469.39,229 319.58,220.51 281.37,220.86 133.39,196 128,195.09 122.41,194.01 \ +116.85,192.84"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to gene association" -> "variant to entity association mixin" [label=uses, - lp="637.89,221.5", - pos="e,388.23,194.1 1647.2,262.15 1385.8,258.18 816.63,247.66 621.39,229 545.55,221.75 460.11,207.45 398.32,195.99"]; + lp="635.89,221.5", + pos="e,386.77,194.22 2624.3,264.36 2216.9,265.02 1011,263.9 619.39,229 543.6,222.24 458.24,207.78 396.8,196.14"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "variant to gene association" -> id [color=blue, label=id, - lp="759.39,221.5", - pos="e,567.12,189.93 1647,262.14 1408.7,258.39 921.53,248.56 752.39,229 677.67,220.36 658.92,215.94 586.39,196 583.24,195.13 580,194.16 \ -576.75,193.13", + lp="755.39,221.5", + pos="e,567.38,190 2625.2,263.09 2204.1,260.05 933.37,249.28 748.39,229 675.35,220.99 657.2,215.65 586.39,196 583.29,195.14 580.09,194.17 \ +576.89,193.16", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "variant to gene association" -> iri [color=blue, label=iri, - lp="881.39,221.5", - pos="e,672,190.19 1645.2,264.75 1467.2,264.37 1146.1,258.96 873.39,229 792.11,220.07 771.72,215.86 692.39,196 688.96,195.14 685.43,194.18 \ -681.89,193.16", + lp="871.39,221.5", + pos="e,672.3,190.23 2624.3,264.53 2249.1,265.52 1205,264.85 863.39,229 786.41,220.92 767.38,215.19 692.39,196 689.02,195.14 685.54,194.18 \ +682.05,193.17", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "variant to gene association" -> name [color=blue, label=name, - lp="989.39,221.5", - pos="e,798.01,190.88 1648.6,261.19 1452.9,256.55 1096.6,246.07 969.39,229 913.26,221.47 850.24,205.52 807.8,193.65", + lp="982.39,221.5", + pos="e,797.01,191.24 2625.3,263.05 2235.3,260.06 1125.3,249.82 962.39,229 908.26,222.08 847.7,206.16 806.73,194.13", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "variant to gene association" -> description [color=blue, label=description, - lp="1112.9,221.5", - pos="e,946.51,193.56 1648.3,261.34 1474.3,257.19 1179.2,247.63 1072.4,229 1032.4,222.03 988.47,208.29 956.15,196.98", + lp="1109.9,221.5", + pos="e,945.41,193.76 2625,263.38 2250.9,261.34 1220.7,253.57 1069.4,229 1029.9,222.58 986.59,208.74 954.87,197.24", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "variant to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="1263.4,221.5", - pos="e,1086.8,191.81 1645.3,264.52 1530.2,262.83 1361.3,255.33 1216.4,229 1174.8,221.45 1128.9,206.77 1096.5,195.27", + lp="1265.4,221.5", + pos="e,1086.6,191.98 2625.4,263.03 2275.1,260.22 1354.9,250.82 1218.4,229 1175.9,222.22 1129.2,207.3 1096.3,195.52", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "variant to gene association" -> subject [color=blue, label=subject, - lp="1407.4,221.5", - pos="e,1235.5,192.43 1654.6,258.51 1575.5,253.7 1472,244.89 1381.4,229 1334.7,220.81 1282.6,206.55 1245.2,195.36", + lp="1420.4,221.5", + pos="e,1235.6,192.36 2624.4,264.28 2327.5,264.28 1628.9,260.78 1394.4,229 1342.9,222.02 1285.4,206.97 1245.2,195.2", style=solid]; negated [color=blue, height=0.5, @@ -87,9 +87,8 @@ digraph { width=1.2999]; "variant to gene association" -> negated [color=blue, label=negated, - lp="1521.4,221.5", - pos="e,1362.6,189.93 1668.8,254.88 1615.1,249.37 1550,241.04 1492.4,229 1442.4,218.56 1431.2,210.87 1382.4,196 1379.1,194.99 1375.7,193.95 \ -1372.2,192.9", + lp="1557.4,221.5", + pos="e,1362.1,190.32 2625,263.46 2350.4,261.83 1736.8,255.27 1528.4,229 1473.6,222.1 1412.3,205.5 1371.9,193.31", style=solid]; qualifiers [color=blue, height=0.5, @@ -98,8 +97,8 @@ digraph { width=2.1304]; "variant to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1629.9,221.5", - pos="e,1502.3,194.24 1695,251.07 1663.6,245.48 1628.1,238.11 1596.4,229 1567.5,220.71 1536.1,208.5 1511.7,198.21", + lp="1691.9,221.5", + pos="e,1510.8,193.12 2624.8,263.51 2372.6,261.96 1840.8,255.55 1658.4,229 1611,222.1 1558.4,207.72 1520.6,196.15", style=solid]; publications [color=blue, height=0.5, @@ -108,8 +107,8 @@ digraph { width=1.7332]; "variant to gene association" -> publications [color=blue, label=publications, - lp="1733.4,221.5", - pos="e,1643.4,195.45 1731.5,248.11 1717.5,242.83 1702.5,236.39 1689.4,229 1676,221.42 1662.3,211.19 1651.1,201.95", + lp="1832.4,221.5", + pos="e,1661,192.88 2624.7,263.49 2396.4,261.89 1945,255.37 1788.4,229 1747.7,222.14 1702.9,207.9 1670.6,196.36", style=solid]; "has evidence" [color=blue, height=0.5, @@ -118,8 +117,8 @@ digraph { width=2.0943]; "variant to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1827.9,221.5", - pos="e,1781.4,196.18 1781.4,246.8 1781.4,235.16 1781.4,219.55 1781.4,206.24", + lp="1982.9,221.5", + pos="e,1817.9,193.89 2625.4,262.67 2426.5,259.96 2064.6,251.96 1936.4,229 1898.8,222.27 1857.8,208.75 1827.4,197.47", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -128,8 +127,8 @@ digraph { width=3.015]; "variant to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1975.9,221.5", - pos="e,1951.1,195.37 1828.6,248.01 1844.6,242.33 1862.4,235.69 1878.4,229 1899.7,220.11 1922.9,209.19 1942.1,199.83", + lp="2127.9,221.5", + pos="e,2003.7,195.77 2627.9,260.94 2440.7,256.06 2115.6,245.39 2063.4,229 2044.8,223.17 2026.3,212 2011.7,201.69", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -138,8 +137,8 @@ digraph { width=3.015]; "variant to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2198.4,221.5", - pos="e,2172,194.37 1879.4,252.49 1940.6,244.99 2013.6,235.44 2044.4,229 2084.3,220.66 2128.4,207.94 2162.3,197.41", + lp="2295.4,221.5", + pos="e,2204.3,196.1 2629.3,260.28 2468.4,255.06 2214.9,244.44 2200.4,229 2194.2,222.38 2195.4,213.47 2199.3,204.99", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -148,9 +147,8 @@ digraph { width=3.015]; "variant to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2460.9,221.5", - pos="e,2414,194.78 1875.7,252 1892.5,250.12 1910,248.36 1926.4,247 2090.9,233.38 2135,258.44 2297.4,229 2334.1,222.34 2374.2,209.36 2404.6,\ -198.29", + lp="2504.9,221.5", + pos="e,2417.2,195.05 2629.9,259.8 2532.6,255.29 2414.1,246.3 2398.4,229 2389.4,219.14 2396.6,209.11 2408.4,200.64", style=solid]; timepoint [color=blue, height=0.5, @@ -159,9 +157,8 @@ digraph { width=1.5346]; "variant to gene association" -> timepoint [color=blue, label=timepoint, - lp="2630.4,221.5", - pos="e,2617.3,195.25 1874.5,251.85 1891.7,249.95 1909.6,248.22 1926.4,247 1997.9,241.82 2503.9,253.28 2571.4,229 2579.8,225.97 2595.7,\ -213.63 2609.5,201.97", + lp="2653.4,221.5", + pos="e,2622.3,195.65 2672.1,251.32 2647.8,245.91 2625.9,238.59 2618.4,229 2612.9,221.97 2614,213.06 2617.6,204.71", style=solid]; "original subject" [color=blue, height=0.5, @@ -170,9 +167,8 @@ digraph { width=1.0652]; "variant to gene association" -> "original subject" [color=blue, label="original subject", - lp="2747.4,221.5", - pos="e,2725.3,192.7 1874.1,251.84 1891.4,249.93 1909.5,248.2 1926.4,247 2008.7,241.19 2589.6,253.46 2668.4,229 2680,225.38 2681.1,220.57 \ -2691.4,214 2699.6,208.79 2708.4,203.21 2716.7,198.07", + lp="2750.4,221.5", + pos="e,2719.7,190.76 2714.2,247.95 2706.3,243.1 2699.1,236.89 2694.4,229 2686.7,216.25 2697.3,204.67 2710.9,195.86", style=solid]; "original predicate" [color=blue, height=0.5, @@ -181,9 +177,8 @@ digraph { width=1.5887]; "variant to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2888.9,221.5", - pos="e,2845.1,195.26 1874.1,251.79 1891.4,249.88 1909.5,248.16 1926.4,247 1975,243.66 2757.9,246.44 2803.4,229 2811.2,226.01 2825.4,213.87 \ -2837.7,202.3", + lp="2887.9,221.5", + pos="e,2843.9,195.61 2783.6,246.94 2791,241.36 2799.1,235.03 2806.4,229 2816.5,220.62 2827.2,211.01 2836.5,202.48", style=solid]; "original object" [color=blue, height=0.5, @@ -192,45 +187,165 @@ digraph { width=1.0652]; "variant to gene association" -> "original object" [color=blue, label="original object", - lp="3017.9,221.5", - pos="e,2972.7,195.97 1873.7,251.79 1891.2,249.87 1909.3,248.15 1926.4,247 1954.9,245.09 2929.6,244.8 2953.4,229 2961.4,223.66 2966.5,\ -214.67 2969.8,205.77", + lp="3018.9,221.5", + pos="e,2972.8,196.36 2851.8,251.67 2898.3,244.67 2946.9,235.94 2955.4,229 2962.5,223.23 2967.1,214.57 2970,206.08", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3108.4,178", + width=2.1304]; + "variant to gene association" -> "subject category" [color=blue, + label="subject category", + lp="3149.9,221.5", + pos="e,3101.3,196.33 2857.9,252.43 2873.8,250.58 2890,248.72 2905.4,247 2942.9,242.8 3042,248.41 3074.4,229 3083.7,223.42 3091.1,214.17 \ +3096.5,205.14", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3279.4,178", + width=2.1304]; + "variant to gene association" -> "object category" [color=blue, + label="object category", + lp="3294.9,221.5", + pos="e,3263.2,195.71 2855.1,252.09 2871.8,250.22 2889.1,248.43 2905.4,247 2973.7,241.01 3149.1,252.73 3213.4,229 3229,223.26 3243.9,212.54 \ +3255.6,202.49", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3412.4,178", + width=1.0652]; + "variant to gene association" -> "subject closure" [color=blue, + label="subject closure", + lp="3432.9,221.5", + pos="e,3399,195.3 2854.3,251.93 2871.3,250.05 2888.8,248.3 2905.4,247 2955.2,243.09 3307.9,247.32 3354.4,229 3368.6,223.4 3381.7,212.78 \ +3391.9,202.75", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3510.4,178", + width=1.0652]; + "variant to gene association" -> "object closure" [color=blue, + label="object closure", + lp="3552.4,221.5", + pos="e,3508.3,196.36 2853.5,251.89 2870.7,249.99 2888.6,248.24 2905.4,247 2937.8,244.6 3463.8,247.64 3490.4,229 3498.1,223.63 3502.8,\ +214.79 3505.7,206.03", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3643.4,178", + width=2.1304]; + "variant to gene association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3710.9,221.5", + pos="e,3635.7,196.2 2853.5,251.82 2870.7,249.92 2888.6,248.2 2905.4,247 2944.3,244.23 3571.8,246.98 3606.4,229 3616.6,223.71 3624.7,214.22 \ +3630.6,204.92", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3833.4,178", + width=2.1304]; + "variant to gene association" -> "object category closure" [color=blue, + label="object category closure", + lp="3900.9,221.5", + pos="e,3827.7,196.13 2853.1,251.78 2870.4,249.88 2888.5,248.16 2905.4,247 2955.1,243.59 3759.1,253.68 3802.4,229 3811.6,223.75 3818.5,\ +214.52 3823.3,205.41", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4023.4,178", + width=1.0652]; + "variant to gene association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4073.4,221.5", + pos="e,4016.4,196.21 2852.7,251.78 2870.2,249.86 2888.3,248.14 2905.4,247 2935.4,245 3961.8,243.12 3988.4,229 3998.2,223.78 4005.9,214.43 \ +4011.5,205.22", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4182.4,178", + width=1.0652]; + "variant to gene association" -> "object namespace" [color=blue, + label="object namespace", + lp="4226.4,221.5", + pos="e,4175,195.75 2852.7,251.75 2870.2,249.83 2888.3,248.12 2905.4,247 2939.8,244.74 4114.7,244.73 4145.4,229 4155.7,223.69 4163.9,214.01 \ +4169.9,204.58", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4333.4,178", + width=1.0652]; + "variant to gene association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4386.4,221.5", + pos="e,4325.4,195.78 2852.7,251.73 2870.2,249.81 2888.3,248.11 2905.4,247 2943.9,244.5 4259.8,246.15 4294.4,229 4305.1,223.68 4313.8,\ +213.86 4320.2,204.32", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4504.4,178", + width=1.0652]; + "variant to gene association" -> "object label closure" [color=blue, + label="object label closure", + lp="4552.9,221.5", + pos="e,4496.1,195.8 2852.7,251.71 2870.2,249.8 2888.3,248.1 2905.4,247 2948.6,244.22 4425.5,247.99 4464.4,229 4475.3,223.7 4484.1,213.89 \ +4490.7,204.35", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4657.4,178", + width=2.347]; + "variant to gene association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4710.9,221.5", + pos="e,4651.7,196.17 2852.3,251.73 2869.9,249.81 2888.2,248.1 2905.4,247 2953.1,243.96 4584.7,252.47 4626.4,229 4635.6,223.79 4642.5,\ +214.57 4647.4,205.46", style=solid]; type [height=0.5, - pos="3063.4,178", + pos="4791.4,178", width=0.86659]; "variant to gene association" -> type [color=blue, label=type, - lp="3095.4,221.5", - pos="e,3073.3,195.53 1873.7,251.76 1891.2,249.85 1909.3,248.13 1926.4,247 1958.2,244.89 3051,251.71 3073.4,229 3079.6,222.67 3079.4,213.63 \ -3076.9,204.98", + lp="4809.4,221.5", + pos="e,4794.1,195.99 2852.3,251.72 2869.9,249.8 2888.2,248.09 2905.4,247 2931.4,245.35 4764.8,246.22 4784.4,229 4790.9,223.33 4793.4,\ +214.66 4794.1,206.12", style=solid]; category [height=0.5, - pos="3164.4,178", + pos="4892.4,178", width=1.4263]; "variant to gene association" -> category [color=blue, label=category, - lp="3168.9,221.5", - pos="e,3153.3,195.87 1873.7,251.76 1891.2,249.84 1909.3,248.13 1926.4,247 1992.3,242.65 3054.7,255.05 3115.4,229 3127.8,223.68 3138.6,\ -213.59 3147,203.85", + lp="4887.9,221.5", + pos="e,4877.7,195.49 2852.3,251.72 2869.9,249.79 2888.2,248.09 2905.4,247 2958.7,243.63 4779,246.83 4829.4,229 4844.6,223.6 4859,212.85 \ +4870.1,202.69", style=solid]; object [height=0.5, pos="1260.4,91", width=1.0832]; "variant to gene association" -> object [color=blue, label=object, - lp="3257.4,178", - pos="e,1299.4,91.832 1873.7,251.74 1891.2,249.83 1909.3,248.12 1926.4,247 1961.8,244.68 3173.6,246.64 3204.4,229 3232.1,213.13 3246.6,\ -182.96 3224.4,160 3155.8,89.028 1606.8,90.799 1309.5,91.797", + lp="4984.4,178", + pos="e,1299.5,91.961 2852.3,251.71 2869.9,249.79 2888.2,248.08 2905.4,247 2961.3,243.48 4872.4,252.34 4923.4,229 4953.6,215.15 4975.7,\ +183.74 4952.4,160 4885.5,91.861 1743.6,91.656 1309.8,91.953", style=solid]; predicate [height=0.5, - pos="3368.4,178", + pos="5096.4,178", width=1.5165]; "variant to gene association" -> predicate [color=blue, label=predicate, - lp="3340.4,221.5", - pos="e,3344.6,194.32 1873.7,251.73 1891.2,249.82 1909.3,248.11 1926.4,247 2000.6,242.16 3193,246.16 3265.4,229 3290.3,223.1 3316.2,210.51 \ -3335.8,199.44", + lp="5068.4,221.5", + pos="e,5072.6,194.36 2852.3,251.71 2869.9,249.78 2888.2,248.08 2905.4,247 3021.2,239.74 4880.5,255.48 4993.4,229 5018.3,223.16 5044.2,\ +210.57 5063.8,199.48", style=solid]; subject -> object [label=relation, lp="1259.4,134.5", @@ -243,23 +358,23 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="1973.4,265", + pos="2952.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2104.4,265", + pos="3083.4,265", width=2.0762]; object -> relation [pos="e,1218.2,35.54 1247.9,73.889 1241,64.939 1232.2,53.617 1224.4,43.584", style=dotted]; "variant to gene association_object" [color=blue, height=0.5, label=gene, - pos="2230.4,265", + pos="3209.4,265", width=0.92075]; "variant to gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2359.4,265", + pos="3338.4,265", width=2.1665]; } diff --git a/graphviz/variant_to_gene_association.svg b/graphviz/variant_to_gene_association.svg index a21ac92d9f..0202a30d45 100644 --- a/graphviz/variant_to_gene_association.svg +++ b/graphviz/variant_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to gene association - -variant to gene association + +variant to gene association @@ -24,9 +24,9 @@ variant to gene association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ variant to gene association->variant to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to gene association->id - - -id + + +id @@ -63,9 +63,9 @@ variant to gene association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ variant to gene association->name - - -name + + +name @@ -89,9 +89,9 @@ variant to gene association->description - - -description + + +description @@ -102,9 +102,9 @@ variant to gene association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ variant to gene association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ variant to gene association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant to gene association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ variant to gene association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ variant to gene association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ variant to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ variant to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ variant to gene association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ variant to gene association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ variant to gene association->original predicate - - -original predicate + + +original predicate @@ -258,110 +258,253 @@ variant to gene association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +variant to gene association->subject category + + +subject category + + + +object category + +ontology class + + + +variant to gene association->object category + + +object category + + + +subject closure + +string + + + +variant to gene association->subject closure + + +subject closure + + + +object closure + +string + + + +variant to gene association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +variant to gene association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +variant to gene association->object category closure + + +object category closure + + + +subject namespace + +string + + + +variant to gene association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +variant to gene association->object namespace + + +object namespace + + + +subject label closure + +string + + + +variant to gene association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +variant to gene association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +variant to gene association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + variant to gene association->type - - -type + + +type - + category - -category + +category - + variant to gene association->category - - -category + + +category - + object object - + variant to gene association->object - - -object + + +object - + predicate - -predicate + +predicate - + variant to gene association->predicate - - -predicate + + +predicate - + subject->object relation - + relation relation - + subject->relation - + association_type - -string + +string - + association_category - -category type + +category type - + object->relation - + variant to gene association_object - -gene + +gene - + variant to gene association_predicate - -predicate type + +predicate type diff --git a/graphviz/variant_to_gene_expression_association.gv b/graphviz/variant_to_gene_expression_association.gv index 78b74368b4..2adcfe7df2 100644 --- a/graphviz/variant_to_gene_expression_association.gv +++ b/graphviz/variant_to_gene_expression_association.gv @@ -1,22 +1,22 @@ digraph { - graph [bb="0,0,4316.7,283"]; + graph [bb="0,0,6032.7,283"]; node [label="\N"]; "variant to gene expression association" [height=0.5, label="variant to gene expression association", - pos="2189.8,265", + pos="3078.8,265", width=5.2537]; "variant to gene association" [height=0.5, pos="135.84,178", width=3.7733]; "variant to gene expression association" -> "variant to gene association" [label=is_a, lp="541.84,221.5", - pos="e,219.31,192.25 2002.4,262.55 1630.1,259.26 809.18,249.85 527.84,229 425.32,221.4 308.51,205.57 229.27,193.74"]; + pos="e,218.54,192.31 2889.6,264.18 2380,264.23 986.65,261.3 527.84,229 424.96,221.76 307.74,205.78 228.5,193.82"]; "gene expression mixin" [height=0.5, pos="404.84,178", width=3.1955]; "variant to gene expression association" -> "gene expression mixin" [label=uses, - lp="674.34,221.5", - pos="e,463.44,193.56 2001.1,263.75 1650.8,262.61 912.47,256.86 657.84,229 594.73,222.1 523.91,207.5 473.29,195.85"]; + lp="673.34,221.5", + pos="e,462.68,193.59 2890.3,263.25 2359.3,260.84 875.94,252.13 656.84,229 593.73,222.34 522.94,207.64 472.49,195.89"]; id [color=blue, height=0.5, label=string, @@ -24,9 +24,9 @@ digraph { width=1.0652]; "variant to gene expression association" -> id [color=blue, label=id, - lp="794.84,221.5", - pos="e,604.82,190.01 2001.3,263.35 1674.7,261.54 1017,254.72 787.84,229 713.95,220.71 695.5,215.79 623.84,196 620.73,195.14 617.53,194.18 \ -614.33,193.17", + lp="792.84,221.5", + pos="e,604.82,190 2890.3,263.13 2379.3,260.5 991.85,251.36 785.84,229 712.79,221.07 694.64,215.65 623.84,196 620.73,195.14 617.53,194.17 \ +614.33,193.16", style=solid]; iri [color=blue, height=0.5, @@ -35,9 +35,9 @@ digraph { width=1.2277]; "variant to gene expression association" -> iri [color=blue, label=iri, - lp="914.84,221.5", - pos="e,709.45,190.17 2002.3,262.5 1698.8,259.47 1113.3,250.92 906.84,229 827.26,220.55 807.42,215.59 729.84,196 726.41,195.13 722.88,\ -194.17 719.34,193.15", + lp="908.84,221.5", + pos="e,709.74,190.23 2891,262.86 2398.6,259.61 1095.4,249.18 900.84,229 823.85,221.01 804.82,215.19 729.84,196 726.46,195.14 722.98,194.18 \ +719.49,193.17", style=solid]; name [color=blue, height=0.5, @@ -46,8 +46,8 @@ digraph { width=1.5707]; "variant to gene expression association" -> name [color=blue, label=name, - lp="1029.8,221.5", - pos="e,835.61,190.94 2002.1,262.77 1718.9,260.17 1195.9,252.29 1009.8,229 952.59,221.83 888.3,205.69 845.27,193.67", + lp="1019.8,221.5", + pos="e,834.45,191.28 2890.4,263.17 2413.6,260.74 1183.9,252.28 999.84,229 945.7,222.15 885.14,206.22 844.17,194.17", style=solid]; description [color=blue, height=0.5, @@ -56,8 +56,8 @@ digraph { width=2.0943]; "variant to gene expression association" -> description [color=blue, label=description, - lp="1155.3,221.5", - pos="e,984.45,193.5 2001.1,263.63 1739.3,262.13 1279.8,255.63 1114.8,229 1073.2,222.27 1027.4,208.29 993.97,196.81", + lp="1146.3,221.5", + pos="e,982.61,193.79 2889.9,263.71 2430.2,262.56 1278.4,256.91 1105.8,229 1066.5,222.64 1023.5,208.8 992.01,197.28", style=solid]; "has attribute" [color=blue, height=0.5, @@ -66,8 +66,8 @@ digraph { width=1.4443]; "variant to gene expression association" -> "has attribute" [color=blue, label="has attribute", - lp="1308.8,221.5", - pos="e,1125,191.7 2002.4,262.38 1773.3,259.45 1399.2,251.32 1261.8,229 1217.7,221.82 1168.8,206.78 1134.6,195.06", + lp="1300.8,221.5", + pos="e,1123.6,192.01 2890.2,263.35 2456.1,261.44 1411.8,254.24 1253.8,229 1211.9,222.29 1165.7,207.37 1133.2,195.56", style=solid]; subject [color=blue, height=0.5, @@ -76,8 +76,8 @@ digraph { width=1.9318]; "variant to gene expression association" -> subject [color=blue, label=subject, - lp="1457.8,221.5", - pos="e,1273.9,192.33 2008.8,259.76 1820.6,254.61 1538.9,244.63 1431.8,229 1380.8,221.55 1323.9,206.77 1283.7,195.2", + lp="1453.8,221.5", + pos="e,1272.6,192.54 2891.5,262.43 2489.6,258.7 1569.3,248.19 1427.8,229 1377.6,222.18 1321.6,207.24 1282.2,195.46", style=solid]; negated [color=blue, height=0.5, @@ -86,8 +86,8 @@ digraph { width=1.2999]; "variant to gene expression association" -> negated [color=blue, label=negated, - lp="1585.8,221.5", - pos="e,1399.1,190.33 2002.3,262.52 1875.9,259.34 1705.6,250.85 1556.8,229 1505.2,221.42 1447.5,205.31 1408.9,193.41", + lp="1587.8,221.5", + pos="e,1398.7,190.46 2889.5,264.6 2540.9,264.88 1810.4,261.39 1558.8,229 1506.3,222.23 1447.5,205.8 1408.6,193.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -96,8 +96,8 @@ digraph { width=2.1304]; "variant to gene expression association" -> qualifiers [color=blue, label=qualifiers, - lp="1716.3,221.5", - pos="e,1547.1,193.28 2006.6,260.46 1909.7,256.3 1789.2,247.49 1682.8,229 1639.6,221.48 1591.7,207.6 1556.6,196.37", + lp="1726.3,221.5", + pos="e,1547.6,193.2 2889.7,264.74 2565.7,265.07 1917.9,261.46 1692.8,229 1646.1,222.26 1594.4,207.87 1557.2,196.25", style=solid]; publications [color=blue, height=0.5, @@ -106,8 +106,8 @@ digraph { width=1.7332]; "variant to gene expression association" -> publications [color=blue, label=publications, - lp="1849.8,221.5", - pos="e,1696.3,193.32 2018.3,257.39 1951.5,252.47 1874.5,243.9 1805.8,229 1771.4,221.52 1733.7,208.14 1705.7,197.11", + lp="1871.8,221.5", + pos="e,1698.6,192.85 2889.6,264.86 2591.6,265.16 2026.3,261.25 1827.8,229 1786.5,222.28 1741,207.95 1708.3,196.35", style=solid]; "has evidence" [color=blue, height=0.5, @@ -116,8 +116,8 @@ digraph { width=2.0943]; "variant to gene expression association" -> "has evidence" [color=blue, label="has evidence", - lp="1989.3,221.5", - pos="e,1850.7,194.37 2061.1,251.76 2022.7,246.5 1980.7,239.15 1942.8,229 1914.5,221.39 1883.8,209.08 1860.1,198.58", + lp="2030.3,221.5", + pos="e,1856.8,193.63 2889.9,263.92 2623.8,262.79 2152.5,256.75 1983.8,229 1943.4,222.35 1899.1,208.52 1866.5,197.09", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -126,8 +126,8 @@ digraph { width=3.015]; "variant to gene expression association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2118.3,221.5", - pos="e,2028.2,196.24 2095.1,249.29 2080.5,244.36 2066.1,237.78 2053.8,229 2045.3,222.9 2038.4,213.84 2033.1,205.1", + lp="2185.3,221.5", + pos="e,2046.4,195.61 2893.2,261.45 2635.7,257.27 2193.3,247.5 2120.8,229 2097.7,223.1 2073.8,211.34 2055.1,200.71", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -136,8 +136,8 @@ digraph { width=3.015]; "variant to gene expression association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2285.8,221.5", - pos="e,2211.5,194.65 2186,246.59 2184.8,236.37 2185,223.63 2190.8,214 2194,208.82 2198.2,204.35 2203,200.52", + lp="2356.8,221.5", + pos="e,2252.8,196.33 2892.1,262.04 2658,258.71 2284.6,250.1 2261.8,229 2255.7,223.32 2253.3,214.91 2252.7,206.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -146,9 +146,8 @@ digraph { width=3.015]; "variant to gene expression association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2510.3,221.5", - pos="e,2447.2,194.64 2304.3,250.65 2330,245.57 2356.8,238.59 2380.8,229 2392.2,224.48 2393,219.64 2403.8,214 2414.6,208.42 2426.4,203.13 \ -2437.7,198.44", + lp="2565.3,221.5", + pos="e,2469,195.87 2897.6,259.78 2720,254.74 2473.9,244.93 2458.8,229 2451.7,221.43 2455.2,212.04 2462,203.46", style=solid]; timepoint [color=blue, height=0.5, @@ -157,9 +156,8 @@ digraph { width=1.5346]; "variant to gene expression association" -> timepoint [color=blue, label=timepoint, - lp="2672.8,221.5", - pos="e,2656.9,195.38 2324.3,252.32 2345.6,250.52 2367.3,248.69 2387.8,247 2438.7,242.82 2569.9,249.05 2616.8,229 2624.3,225.83 2637.6,\ -214.02 2649.4,202.68", + lp="2719.8,221.5", + pos="e,2672.2,196.43 2905.1,257.84 2807.6,252.76 2702.1,243.9 2684.8,229 2678.3,223.36 2675,214.85 2673.4,206.44", style=solid]; "original subject" [color=blue, height=0.5, @@ -168,9 +166,8 @@ digraph { width=1.0652]; "variant to gene expression association" -> "original subject" [color=blue, label="original subject", - lp="2787.8,221.5", - pos="e,2763.7,193.27 2322.1,252.09 2344.1,250.27 2366.6,248.51 2387.8,247 2459.3,241.93 2641.9,251.67 2709.8,229 2711.2,228.55 2734.9,\ -212.71 2755.3,198.97", + lp="2817.8,221.5", + pos="e,2769.1,194.82 2917.6,255.54 2845,250.05 2773.1,241.53 2761.8,229 2755.2,221.56 2757.8,211.85 2763.2,202.97", style=solid]; "original predicate" [color=blue, height=0.5, @@ -179,9 +176,8 @@ digraph { width=1.5887]; "variant to gene expression association" -> "original predicate" [color=blue, label="original predicate", - lp="2928.3,221.5", - pos="e,2883.5,195.47 2320.2,251.94 2342.8,250.1 2366,248.37 2387.8,247 2438.6,243.83 2797.9,248.47 2844.8,229 2852.1,225.97 2865,214.16 \ -2876.4,202.79", + lp="2944.3,221.5", + pos="e,2885.1,195.79 2941.3,252.62 2913.5,247.45 2890,239.93 2880.8,229 2875,222.04 2876.3,213.05 2880.1,204.61", style=solid]; "original object" [color=blue, height=0.5, @@ -190,87 +186,204 @@ digraph { width=1.0652]; "variant to gene expression association" -> "original object" [color=blue, label="original object", - lp="3058.3,221.5", - pos="e,3011.5,196.31 2319.2,251.85 2342,250 2365.6,248.28 2387.8,247 2421.5,245.06 2967.5,248.81 2994.8,229 3002.2,223.63 3006.6,214.91 \ -3009.2,206.25", + lp="3068.3,221.5", + pos="e,3010.4,196.01 3036.2,247.37 3028.6,242.55 3021.6,236.5 3016.8,229 3012.5,222.26 3010.8,213.93 3010.4,206.01", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3145.8,178", + width=2.1304]; + "variant to gene expression association" -> "subject category" [color=blue, + label="subject category", + lp="3189.3,221.5", + pos="e,3138.9,196.18 3102,246.89 3108.3,241.6 3114.7,235.45 3119.8,229 3125.5,221.84 3130.5,213.25 3134.6,205.22", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3316.8,178", + width=2.1304]; + "variant to gene expression association" -> "object category" [color=blue, + label="object category", + lp="3333.3,221.5", + pos="e,3300.1,195.66 3187.6,250.21 3209.8,245.18 3232.5,238.33 3252.8,229 3267.2,222.41 3281.2,212.04 3292.4,202.44", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3449.8,178", + width=1.0652]; + "variant to gene expression association" -> "subject closure" [color=blue, + label="subject closure", + lp="3470.3,221.5", + pos="e,3436.6,194.94 3216,252.54 3292.7,245.45 3376.2,236.33 3392.8,229 3406.7,222.9 3419.5,212.23 3429.6,202.3", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3547.8,178", + width=1.0652]; + "variant to gene expression association" -> "object closure" [color=blue, + label="object closure", + lp="3589.8,221.5", + pos="e,3545.6,196.23 3212.7,252.25 3234.2,250.44 3256.1,248.63 3276.8,247 3304.7,244.8 3505.3,245.49 3527.8,229 3535.3,223.53 3540,214.79 \ +3542.9,206.14", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3680.8,178", + width=2.1304]; + "variant to gene expression association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3748.3,221.5", + pos="e,3673.1,196.1 3210.3,252.03 3232.5,250.21 3255.3,248.45 3276.8,247 3317.6,244.25 3607.8,248.26 3643.8,229 3653.9,223.59 3662,214.08 \ +3668,204.79", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3870.8,178", + width=2.1304]; + "variant to gene expression association" -> "object category closure" [color=blue, + label="object category closure", + lp="3938.3,221.5", + pos="e,3865.1,196.09 3208.4,251.87 3231.2,250.02 3254.7,248.3 3276.8,247 3308.1,245.16 3812.7,244.65 3839.8,229 3849,223.69 3855.9,214.45 \ +3860.7,205.35", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4060.8,178", + width=1.0652]; + "variant to gene expression association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4110.8,221.5", + pos="e,4053.8,196.18 3207.6,251.78 3230.7,249.93 3254.4,248.23 3276.8,247 3318.4,244.72 3989.2,248.66 4025.8,229 4035.6,223.74 4043.3,\ +214.39 4048.9,205.18", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4219.8,178", + width=1.0652]; + "variant to gene expression association" -> "object namespace" [color=blue, + label="object namespace", + lp="4263.8,221.5", + pos="e,4212.5,195.73 3207.1,251.75 3230.3,249.89 3254.3,248.19 3276.8,247 3327.1,244.35 4138.1,252.1 4182.8,229 4193.2,223.67 4201.3,\ +213.98 4207.4,204.55", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4370.8,178", + width=1.0652]; + "variant to gene expression association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4423.8,221.5", + pos="e,4362.8,195.76 3206.8,251.72 3230.1,249.85 3254.2,248.16 3276.8,247 3335.4,243.99 4279.4,255.17 4331.8,229 4342.5,223.66 4351.2,\ +213.83 4357.6,204.3", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4541.8,178", + width=1.0652]; + "variant to gene expression association" -> "object label closure" [color=blue, + label="object label closure", + lp="4589.3,221.5", + pos="e,4533.5,195.78 3206.6,251.69 3229.9,249.83 3254.1,248.14 3276.8,247 3310.8,245.29 4471.3,243.97 4501.8,229 4512.7,223.68 4521.5,\ +213.87 4528.1,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4682.8,178", + width=2.347]; + "variant to gene expression association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4744.3,221.5", + pos="e,4680.8,196.42 3206.3,251.68 3229.7,249.81 3254,248.13 3276.8,247 3315.3,245.1 4631.1,250.79 4662.8,229 4670.6,223.69 4675.3,214.87 \ +4678.2,206.11", style=solid]; type [height=0.5, - pos="3100.8,178", + pos="4816.8,178", width=0.86659]; "variant to gene expression association" -> type [color=blue, label=type, - lp="3134.8,221.5", - pos="e,3111.8,194.96 2318.6,251.8 2341.7,249.94 2365.4,248.24 2387.8,247 2408,245.89 3099.8,243.44 3113.8,229 3120.3,222.4 3119.4,213.04 \ -3116.1,204.19", + lp="4840.8,221.5", + pos="e,4822.8,196.12 3206.3,251.66 3229.7,249.79 3254,248.11 3276.8,247 3298.2,245.96 4802.8,244.22 4817.8,229 4823.7,223.03 4825,214.44 \ +4824.4,206.05", style=solid]; category [height=0.5, - pos="3201.8,178", + pos="4917.8,178", width=1.4263]; "variant to gene expression association" -> category [color=blue, label=category, - lp="3208.3,221.5", - pos="e,3191.4,195.81 2318.6,251.77 2341.7,249.92 2365.4,248.22 2387.8,247 2430.4,244.68 3115.9,246.38 3154.8,229 3166.9,223.61 3177.3,\ -213.5 3185.3,203.78", + lp="4917.3,221.5", + pos="e,4904.8,195.44 3206,251.67 3229.6,249.79 3253.9,248.11 3276.8,247 3320.8,244.87 4819.7,244.74 4860.8,229 4874.9,223.6 4887.9,212.99 \ +4897.8,202.93", style=solid]; object [height=0.5, pos="1297.8,91", width=1.0832]; "variant to gene expression association" -> object [color=blue, label=object, - lp="3295.8,178", - pos="e,1336.9,91.832 2318.1,251.77 2341.3,249.91 2365.3,248.2 2387.8,247 2435.3,244.46 3203.2,253.71 3243.8,229 3270.9,212.54 3283.9,\ -182.79 3261.8,160 3193.3,89.028 1644.2,90.799 1346.9,91.797", + lp="5010.8,178", + pos="e,1336.8,91.963 3206,251.66 3229.5,249.78 3253.9,248.11 3276.8,247 3323.3,244.76 4911.3,249.94 4952.8,229 4982,214.33 5000.7,183.28 \ +4977.8,160 4911.2,92.08 1779.4,91.687 1347.1,91.956", style=solid]; predicate [height=0.5, - pos="3405.8,178", + pos="5121.8,178", width=1.5165]; "variant to gene expression association" -> predicate [color=blue, label=predicate, - lp="3378.8,221.5", - pos="e,3382,194.28 2318.1,251.75 2341.3,249.88 2365.3,248.19 2387.8,247 2489.4,241.65 3204,252.76 3302.8,229 3327.7,223.03 3353.6,210.43 \ -3373.2,199.38", + lp="5094.8,221.5", + pos="e,5098,194.35 3206,251.65 3229.5,249.78 3253.9,248.1 3276.8,247 3373.5,242.36 4924.6,251.17 5018.8,229 5043.7,223.14 5069.6,210.55 \ +5089.2,199.47", style=solid]; "quantifier qualifier" [height=0.5, - pos="3575.8,178", + pos="5291.8,178", width=2.7081]; "variant to gene expression association" -> "quantifier qualifier" [color=blue, label="quantifier qualifier", - lp="3546.8,221.5", - pos="e,3537.1,194.64 2317.8,251.73 2341.1,249.86 2365.2,248.17 2387.8,247 2502,241.11 3304,247.34 3416.8,229 3454.9,222.82 3496.3,209.55 \ -3527.4,198.24", + lp="5262.8,221.5", + pos="e,5253.4,194.61 3206,251.64 3229.5,249.77 3253.9,248.09 3276.8,247 3482.8,237.17 4929.1,261.28 5132.8,229 5171,222.95 5212.6,209.61 \ +5243.7,198.22", style=solid]; "expression site" [color=blue, height=0.5, label="anatomical entity", - pos="3782.8,178", + pos="5498.8,178", width=2.5456]; "variant to gene expression association" -> "expression site" [color=blue, label="expression site", - lp="3737.3,221.5", - pos="e,3743.6,194.31 2317.6,251.69 2340.9,249.82 2365.1,248.14 2387.8,247 2524.3,240.15 3482.8,250.02 3617.8,229 3657.8,222.78 3701.5,\ -209.21 3733.9,197.78", + lp="5453.3,221.5", + pos="e,5459.6,194.38 3205.8,251.65 3229.4,249.76 3253.8,248.09 3276.8,247 3391,241.61 5220.9,246.25 5333.8,229 5373.8,222.9 5417.5,209.32 \ +5449.9,197.86", style=solid]; "stage qualifier" [color=blue, height=0.5, label="life stage", - pos="3946.8,178", + pos="5662.8,178", width=1.4985]; "variant to gene expression association" -> "stage qualifier" [color=blue, label="stage qualifier", - lp="3907.3,221.5", - pos="e,3915.2,192.66 2317.3,251.68 2340.7,249.81 2365,248.12 2387.8,247 2544.1,239.3 3641.5,254.89 3795.8,229 3834,222.59 3875.6,208.22 \ -3905.5,196.51", + lp="5623.3,221.5", + pos="e,5631.2,192.71 3205.8,251.63 3229.4,249.75 3253.8,248.08 3276.8,247 3400.9,241.18 5389.3,249.26 5511.8,229 5550,222.68 5591.7,208.3 \ +5621.5,196.57", style=solid]; "phenotypic state" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="4167.8,178", + pos="5883.8,178", width=4.1344]; "variant to gene expression association" -> "phenotypic state" [color=blue, label="phenotypic state", - lp="4101.8,221.5", - pos="e,4116.6,194.94 2317,251.68 2340.6,249.8 2364.9,248.11 2387.8,247 2562.6,238.51 3789.2,250.88 3962.8,229 4012,222.8 4066.5,209.18 \ -4106.9,197.72", + lp="5817.8,221.5", + pos="e,5832.6,194.99 3205.8,251.62 3229.4,249.74 3253.8,248.07 3276.8,247 3543.4,234.57 5414,261.84 5678.8,229 5728,222.9 5782.5,209.27 \ +5822.9,197.79", style=solid]; subject -> object [label=relation, lp="1296.8,134.5", @@ -283,28 +396,28 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2434.8,265", + pos="3323.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2565.8,265", + pos="3454.8,265", width=2.0762]; object -> relation [pos="e,1255.7,35.54 1285.4,73.889 1278.4,64.939 1269.7,53.617 1261.9,43.584", style=dotted]; "variant to gene association_object" [color=blue, height=0.5, label=gene, - pos="2691.8,265", + pos="3580.8,265", width=0.92075]; "variant to gene expression association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2820.8,265", + pos="3709.8,265", width=2.1665]; "gene expression mixin_quantifier qualifier" [color=blue, height=0.5, label="ontology class", - pos="2993.8,265", + pos="3882.8,265", width=2.1304]; } diff --git a/graphviz/variant_to_gene_expression_association.svg b/graphviz/variant_to_gene_expression_association.svg index 8d6c1c078d..a3314302cc 100644 --- a/graphviz/variant_to_gene_expression_association.svg +++ b/graphviz/variant_to_gene_expression_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to gene expression association - -variant to gene expression association + +variant to gene expression association @@ -24,8 +24,8 @@ variant to gene expression association->variant to gene association - - + + is_a @@ -37,9 +37,9 @@ variant to gene expression association->gene expression mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to gene expression association->id - - -id + + +id @@ -63,9 +63,9 @@ variant to gene expression association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ variant to gene expression association->name - - -name + + +name @@ -89,9 +89,9 @@ variant to gene expression association->description - - -description + + +description @@ -102,9 +102,9 @@ variant to gene expression association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ variant to gene expression association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ variant to gene expression association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant to gene expression association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant to gene expression association->publications - - -publications + + +publications @@ -167,9 +167,9 @@ variant to gene expression association->has evidence - - -has evidence + + +has evidence @@ -180,9 +180,9 @@ variant to gene expression association->knowledge source - - -knowledge source + + +knowledge source @@ -193,9 +193,9 @@ variant to gene expression association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -206,9 +206,9 @@ variant to gene expression association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -219,9 +219,9 @@ variant to gene expression association->timepoint - - -timepoint + + +timepoint @@ -232,9 +232,9 @@ variant to gene expression association->original subject - - -original subject + + +original subject @@ -245,9 +245,9 @@ variant to gene expression association->original predicate - - -original predicate + + +original predicate @@ -258,168 +258,311 @@ variant to gene expression association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +variant to gene expression association->subject category + + +subject category + + + +object category + +ontology class + + + +variant to gene expression association->object category + + +object category + + + +subject closure + +string + + + +variant to gene expression association->subject closure + + +subject closure + + + +object closure + +string + + + +variant to gene expression association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +variant to gene expression association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +variant to gene expression association->object category closure + + +object category closure + + + +subject namespace + +string + + + +variant to gene expression association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +variant to gene expression association->object namespace + + +object namespace + + + +subject label closure + +string + + + +variant to gene expression association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +variant to gene expression association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +variant to gene expression association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + variant to gene expression association->type - - -type + + +type - + category - -category + +category - + variant to gene expression association->category - - -category + + +category - + object object - + variant to gene expression association->object - - -object + + +object - + predicate - -predicate + +predicate - + variant to gene expression association->predicate - - -predicate + + +predicate - + quantifier qualifier - -quantifier qualifier + +quantifier qualifier - + variant to gene expression association->quantifier qualifier - - -quantifier qualifier + + +quantifier qualifier - + expression site - -anatomical entity + +anatomical entity - + variant to gene expression association->expression site - - -expression site + + +expression site - + stage qualifier - -life stage + +life stage - + variant to gene expression association->stage qualifier - - -stage qualifier + + +stage qualifier - + phenotypic state - -disease or phenotypic feature + +disease or phenotypic feature - + variant to gene expression association->phenotypic state - - -phenotypic state + + +phenotypic state - + subject->object relation - + relation relation - + subject->relation - + association_type - -string + +string - + association_category - -category type + +category type - + object->relation - + variant to gene association_object - -gene + +gene - + variant to gene expression association_predicate - -predicate type + +predicate type - + gene expression mixin_quantifier qualifier - -ontology class + +ontology class diff --git a/graphviz/variant_to_phenotypic_feature_association.gv b/graphviz/variant_to_phenotypic_feature_association.gv index d3221de7f5..624dd095fe 100644 --- a/graphviz/variant_to_phenotypic_feature_association.gv +++ b/graphviz/variant_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,4953.4,283"]; + graph [bb="0,0,6615.4,283"]; node [label="\N"]; "variant to phenotypic feature association" [height=0.5, label="variant to phenotypic feature association", - pos="2826.4,265", + pos="3665.4,265", width=5.5967]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to phenotypic feature association" -> association [label=is_a, - lp="683.39,221.5", - pos="e,106.48,190.81 2625.2,263.77 2243.7,262.67 1388.6,256.96 669.39,229 430.9,219.73 369.45,231.25 133.39,196 127.91,195.18 122.23,\ -194.15 116.57,192.99"]; + lp="661.39,221.5", + pos="e,106.48,190.79 3465,263.05 2882.8,260.08 1198.3,249.87 647.39,229 418.64,220.34 359.75,230.11 133.39,196 127.91,195.17 122.23,194.13 \ +116.57,192.98"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to phenotypic feature association" -> "variant to entity association mixin" [label=uses, - lp="933.89,221.5", - pos="e,429.35,191.08 2624.9,264.21 2276.6,263.7 1539.4,258.77 917.39,229 752.03,221.09 561.81,204.06 439.5,192.08"]; + lp="924.89,221.5", + pos="e,427.32,191.24 3464.9,263.18 2917.7,260.67 1406.2,251.83 908.39,229 745.33,221.52 557.79,204.37 437.32,192.25"]; "entity to phenotypic feature association mixin" [height=0.5, pos="724.39,178", width=6.2286]; "variant to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, - lp="1098.9,221.5", - pos="e,814.19,194.55 2625.9,262.97 2233.5,260.46 1376.5,252.41 1082.4,229 994.71,222.02 895.73,207.7 824.11,196.16"]; + lp="1100.9,221.5", + pos="e,813.57,194.53 3463.5,264.51 2939.7,265.32 1545.3,264 1084.4,229 995.76,222.27 895.66,207.81 823.55,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "variant to phenotypic feature association" -> id [color=blue, label=id, - lp="1214.4,221.5", - pos="e,1034.4,189.95 2624.8,264.41 2253.6,264.36 1475.7,260.36 1207.4,229 1137.9,220.87 1120.7,215.06 1053.4,196 1050.3,195.12 1047.1,\ -194.15 1043.9,193.12", + lp="1218.4,221.5", + pos="e,1034.4,189.97 3464.6,263.35 2918.5,261.26 1431.9,253.38 1211.4,229 1140.1,221.12 1122.5,215.35 1053.4,196 1050.3,195.13 1047.1,\ +194.16 1043.9,193.14", style=solid]; iri [color=blue, height=0.5, @@ -43,8 +43,7 @@ digraph { "variant to phenotypic feature association" -> iri [color=blue, label=iri, lp="1315.4,221.5", - pos="e,1139.3,190.08 2624.8,264.26 2271.9,263.9 1556.1,259.29 1307.4,229 1240.5,220.85 1224.4,213.64 1159.4,196 1156,195.09 1152.6,194.09 \ -1149.1,193.06", + pos="e,1139.7,190.05 3464.4,263.37 2933.1,261.38 1518.1,253.79 1307.4,229 1251.9,222.47 1189.8,205.46 1149.5,193.09", style=solid]; name [color=blue, height=0.5, @@ -54,7 +53,7 @@ digraph { "variant to phenotypic feature association" -> name [color=blue, label=name, lp="1411.4,221.5", - pos="e,1259.7,192.3 2627.2,262.1 2261.5,258.18 1509.8,247.93 1391.4,229 1349.1,222.24 1302.5,207.55 1269.5,195.83", + pos="e,1259.7,192.4 3463.9,264.09 2945.6,263.85 1592.6,260.22 1391.4,229 1349.1,222.43 1302.5,207.72 1269.5,195.95", style=solid]; description [color=blue, height=0.5, @@ -64,7 +63,7 @@ digraph { "variant to phenotypic feature association" -> description [color=blue, label=description, lp="1514.9,221.5", - pos="e,1399.8,195.2 2625.4,263.66 2275.8,262.34 1582.6,256.26 1474.4,229 1451.1,223.14 1427.1,211.14 1408.5,200.36", + pos="e,1399.8,195.28 3464.9,263.23 2941.9,260.9 1569.9,252.56 1474.4,229 1451.1,223.25 1427,211.26 1408.5,200.45", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +73,7 @@ digraph { "variant to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1634.4,221.5", - pos="e,1536.3,195.39 2624.6,264.95 2298.5,265.48 1682.3,262.01 1587.4,229 1571.4,223.42 1556,212.5 1544,202.28", + pos="e,1536,195.21 3464,263.95 2959.5,263.36 1675.1,258.93 1587.4,229 1571.2,223.48 1555.7,212.45 1543.7,202.15", style=solid]; predicate [color=blue, height=0.5, @@ -84,18 +83,18 @@ digraph { "variant to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1734.4,221.5", - pos="e,1674.4,196.11 2626.5,262.6 2313.7,259.71 1739.8,251.39 1700.4,229 1691,223.66 1683.9,214.29 1678.8,205.09", + pos="e,1674.4,196.16 3465.2,262.91 2972.6,259.92 1738.5,250.3 1700.4,229 1690.9,223.72 1683.9,214.36 1678.8,205.16", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="3744.4,91", + pos="5406.4,91", width=1.9318]; "variant to phenotypic feature association" -> object [color=blue, label=object, lp="1813.4,178", - pos="e,3674.7,91.747 2628.4,261.62 2462,258.17 2218.2,249.72 2006.4,229 1906.5,219.23 1721.7,232.19 1791.4,160 1857.5,91.603 3306,90.853 \ -3664.6,91.721", + pos="e,5336.7,91.969 3464.8,263.06 3087.2,260.76 2283.6,253.1 2006.4,229 1906.4,220.31 1721.1,231.63 1791.4,160 1855.5,94.718 4801.1,\ +91.943 5326.6,91.968", style=solid]; negated [color=blue, height=0.5, @@ -105,7 +104,7 @@ digraph { "variant to phenotypic feature association" -> negated [color=blue, label=negated, lp="2114.4,221.5", - pos="e,1925.6,190.31 2636.3,259.04 2452.6,253.51 2187.7,243.43 2085.4,229 2033.1,221.62 1974.5,205.39 1935.6,193.41", + pos="e,1925.2,190.47 3463.6,264.82 3099.3,265.43 2345.7,262.4 2085.4,229 2032.8,222.25 1974.1,205.82 1935.2,193.63", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +113,8 @@ digraph { width=2.1304]; "variant to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2244.9,221.5", - pos="e,2073.8,193.3 2625.4,263.46 2504.7,260.44 2348.4,251.76 2211.4,229 2167.5,221.7 2118.9,207.74 2083.4,196.42", + lp="2253.9,221.5", + pos="e,2074.4,193.22 3467,261.79 3099.7,257.32 2340.2,246.13 2220.4,229 2173.4,222.28 2121.4,207.89 2084,196.26", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +123,8 @@ digraph { width=1.7332]; "variant to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2378.4,221.5", - pos="e,2222.7,193.27 2628.2,261.66 2537.8,257.6 2429.9,248.52 2334.4,229 2299.2,221.8 2260.7,208.28 2232.3,197.11", + lp="2400.4,221.5", + pos="e,2225.2,192.74 3467.5,261.59 3128.5,257.02 2462.7,246.03 2356.4,229 2314.2,222.25 2267.8,207.75 2234.7,196.1", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,8 +133,8 @@ digraph { width=2.0943]; "variant to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2518.9,221.5", - pos="e,2377.2,194.38 2650.1,256.21 2592.9,251.13 2529.4,242.76 2472.4,229 2442.8,221.86 2410.9,209.3 2386.5,198.55", + lp="2559.9,221.5", + pos="e,2383.8,193.52 3464,264.14 3183.7,263.26 2690.3,257.52 2513.4,229 2472,222.32 2426.4,208.33 2393.2,196.84", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -144,8 +143,8 @@ digraph { width=3.015]; "variant to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2649.9,221.5", - pos="e,2555.9,196.21 2683.4,252.32 2641.9,246.96 2603.1,239.41 2585.4,229 2575.6,223.21 2567.4,213.81 2561.2,204.71", + lp="2715.9,221.5", + pos="e,2574,195.62 3467.6,261.54 3194.8,257.48 2728.1,247.87 2651.4,229 2627.4,223.09 2602.3,211.25 2582.9,200.58", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -154,8 +153,8 @@ digraph { width=3.015]; "variant to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2816.4,221.5", - pos="e,2741.3,194.83 2744.3,248.46 2735.3,243.6 2727.3,237.26 2721.4,229 2713.5,218.08 2720.7,208.17 2732.5,200.11", + lp="2888.4,221.5", + pos="e,2781.3,196.06 3466.4,262.1 3217,258.82 2818.8,250.28 2793.4,229 2786.7,223.4 2783.5,214.75 2782.2,206.21", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -164,9 +163,8 @@ digraph { width=3.015]; "variant to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3040.9,221.5", - pos="e,2976.2,194.67 2871.2,247.37 2884.4,242 2898.7,235.69 2911.4,229 2922.2,223.32 2923.6,219.73 2934.4,214 2944.6,208.55 2955.9,203.32 \ -2966.8,198.64", + lp="3097.9,221.5", + pos="e,2999.2,195.77 3470.6,260.37 3277.4,255.8 3007.9,246.34 2991.4,229 2984.6,221.79 2987.2,212.44 2993,203.77", style=solid]; timepoint [color=blue, height=0.5, @@ -175,8 +173,8 @@ digraph { width=1.5346]; "variant to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3204.4,221.5", - pos="e,3186.8,195.92 2971.6,252.48 3048.7,245.58 3130.9,236.7 3147.4,229 3159.8,223.2 3171.1,213.23 3180,203.71", + lp="3254.4,221.5", + pos="e,3201.6,196.2 3477.6,258.47 3365.4,253.57 3240.7,244.66 3219.4,229 3211.9,223.5 3207.2,214.76 3204.3,206.11", style=solid]; "original subject" [color=blue, height=0.5, @@ -185,8 +183,8 @@ digraph { width=1.0652]; "variant to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3318.4,221.5", - pos="e,3291.2,193.59 2969.6,252.32 3088,242.61 3237.1,230.19 3240.4,229 3242.9,228.09 3264.3,212.94 3282.9,199.55", + lp="3353.4,221.5", + pos="e,3299.9,195.21 3482.7,257.37 3397,252.34 3310.7,243.67 3297.4,229 3291.2,222.24 3292.2,213 3295.5,204.3", style=solid]; "original predicate" [color=blue, height=0.5, @@ -195,9 +193,8 @@ digraph { width=1.5887]; "variant to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3459.9,221.5", - pos="e,3414,195.69 2967.4,252.11 2990.8,250.29 3014.8,248.51 3037.4,247 3074.9,244.49 3341,244.31 3375.4,229 3387.8,223.46 3398.9,213.33 \ -3407.4,203.63", + lp="3481.9,221.5", + pos="e,3416.9,196.2 3492.4,255.76 3458.5,250.51 3429.8,242.16 3418.4,229 3412.9,222.69 3412.5,214.16 3414.1,205.92", style=solid]; "original object" [color=blue, height=0.5, @@ -206,148 +203,264 @@ digraph { width=1.0652]; "variant to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3587.9,221.5", - pos="e,3539.4,196.17 2965.4,251.94 2989.4,250.1 3014.1,248.37 3037.4,247 3064.5,245.41 3504.1,245.79 3525.4,229 3532.4,223.47 3536.1,\ -214.71 3538,206.07", + lp="3610.9,221.5", + pos="e,3542.5,196.4 3589.8,248.23 3578.7,243.43 3568.1,237.16 3559.4,229 3552.9,222.9 3548.5,214.41 3545.5,206.17", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3672.4,178", + width=2.1304]; + "variant to phenotypic feature association" -> "subject category" [color=blue, + label="subject category", + lp="3725.9,221.5", + pos="e,3669,196.02 3665.1,246.84 3665.1,237.17 3665.4,224.89 3666.4,214 3666.6,211.42 3667,208.75 3667.3,206.08", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3843.4,178", + width=2.1304]; + "variant to phenotypic feature association" -> "object category" [color=blue, + label="object category", + lp="3861.9,221.5", + pos="e,3827.6,195.97 3738.1,248.2 3754.2,243.24 3770.8,236.92 3785.4,229 3797.9,222.19 3810.1,212.3 3820.1,203.12", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3976.4,178", + width=1.0652]; + "variant to phenotypic feature association" -> "subject closure" [color=blue, + label="subject closure", + lp="3993.9,221.5", + pos="e,3960.8,194.48 3804.4,251.93 3851.8,246.31 3898.2,238.69 3919.4,229 3927,225.51 3941.2,213.09 3953.5,201.5", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4072.4,178", + width=1.0652]; + "variant to phenotypic feature association" -> "object closure" [color=blue, + label="object closure", + lp="4113.4,221.5", + pos="e,4069.8,196.19 3805.9,252.09 3915.2,242.7 4048.8,230.87 4051.4,229 4059,223.42 4063.9,214.55 4067,205.81", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4205.4,178", + width=2.1304]; + "variant to phenotypic feature association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4271.9,221.5", + pos="e,4197.3,196.06 3807.2,252.21 3830.3,250.39 3854,248.59 3876.4,247 3908.7,244.7 4138.8,244.28 4167.4,229 4177.6,223.54 4185.9,214.02 \ +4192.1,204.74", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4394.4,178", + width=2.1304]; + "variant to phenotypic feature association" -> "object category closure" [color=blue, + label="object category closure", + lp="4461.9,221.5", + pos="e,4388.7,196.07 3804.4,251.94 3828.4,250.1 3853.1,248.37 3876.4,247 3903.4,245.41 4340,242.6 4363.4,229 4372.6,223.67 4379.4,214.43 \ +4384.3,205.33", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4584.4,178", + width=1.0652]; + "variant to phenotypic feature association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4634.4,221.5", + pos="e,4577.4,196.17 3802.9,251.85 3827.4,249.99 3852.6,248.27 3876.4,247 3913.7,245 4516.5,246.71 4549.4,229 4559.2,223.73 4566.8,214.37 \ +4572.5,205.17", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4743.4,178", + width=1.0652]; + "variant to phenotypic feature association" -> "object namespace" [color=blue, + label="object namespace", + lp="4787.4,221.5", + pos="e,4736,195.72 3802.4,251.79 3827,249.93 3852.4,248.22 3876.4,247 3922.5,244.65 4665.4,250.2 4706.4,229 4716.7,223.66 4724.9,213.97 \ +4730.9,204.54", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4894.4,178", + width=1.0652]; + "variant to phenotypic feature association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4947.4,221.5", + pos="e,4886.4,195.76 3802.1,251.74 3826.8,249.88 3852.4,248.19 3876.4,247 3930.7,244.31 4806.7,253.31 4855.4,229 4866.1,223.65 4874.7,\ +213.83 4881.2,204.29", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5014.4,178", + width=1.0652]; + "variant to phenotypic feature association" -> "object label closure" [color=blue, + label="object label closure", + lp="5100.9,221.5", + pos="e,5024.7,195.5 3801.8,251.71 3826.6,249.85 3852.3,248.16 3876.4,247 3908.3,245.47 5003,251.75 5025.4,229 5031.6,222.65 5031.3,213.6 \ +5028.6,204.95", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5155.4,178", + width=2.347]; + "variant to phenotypic feature association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5248.9,221.5", + pos="e,5170.2,196.21 3801.5,251.7 3826.4,249.83 3852.2,248.14 3876.4,247 3894.4,246.15 5161.7,241.84 5174.4,229 5180.9,222.42 5179.5,\ +213.41 5175.3,204.85", style=solid]; type [height=0.5, - pos="3627.4,178", + pos="5289.4,178", width=0.86659]; "variant to phenotypic feature association" -> type [color=blue, label=type, - lp="3664.4,221.5", - pos="e,3639.7,194.86 2964.5,251.86 2988.8,250.02 3013.8,248.3 3037.4,247 3071,245.15 3619.9,253.17 3643.4,229 3650,222.2 3648.6,212.69 \ -3644.6,203.78", + lp="5343.4,221.5", + pos="e,5308.1,192.56 3801.2,251.69 3826.2,249.81 3852.1,248.13 3876.4,247 3896.5,246.07 5308.3,243.29 5322.4,229 5331,220.33 5324.8,209.13 \ +5315.5,199.52", style=solid]; category [height=0.5, - pos="3728.4,178", + pos="5390.4,178", width=1.4263]; "variant to phenotypic feature association" -> category [color=blue, label=category, - lp="3734.9,221.5", - pos="e,3718.8,195.77 2964.2,251.85 2988.6,250 3013.7,248.28 3037.4,247 3073.3,245.06 3651.8,244.27 3684.4,229 3695.9,223.61 3705.6,213.64 \ -3713,204.01", + lp="5408.9,221.5", + pos="e,5386.1,196.09 3801.2,251.68 3826.2,249.81 3852.1,248.13 3876.4,247 3917.7,245.09 5328,250.38 5363.4,229 5372.1,223.75 5378.1,214.65 \ +5382.3,205.65", style=solid]; subject [height=0.5, - pos="3842.4,178", + pos="5504.4,178", width=1.2277]; "variant to phenotypic feature association" -> subject [color=blue, label=subject, - lp="3826.4,221.5", - pos="e,3825.6,194.94 2963.9,251.8 2988.4,249.95 3013.6,248.25 3037.4,247 3118.8,242.73 3693,254.3 3770.4,229 3787.7,223.34 3804.6,212.03 \ -3817.6,201.6", + lp="5496.4,221.5", + pos="e,5490.5,195.46 3801.2,251.67 3826.2,249.8 3852.1,248.12 3876.4,247 3919.9,245 5403.5,244.06 5444.4,229 5459.1,223.57 5472.8,212.81 \ +5483.4,202.66", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="3989.4,178", + pos="5651.4,178", width=2.3651]; "variant to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="3977.4,221.5", - pos="e,3957,194.73 2963.4,251.79 2988,249.93 3013.4,248.23 3037.4,247 3128.3,242.34 3767,246.26 3856.4,229 3888,222.9 3921.9,210.05 3947.5,\ -198.91", + lp="5644.4,221.5", + pos="e,5621,194.84 3800.9,251.68 3826,249.8 3852,248.12 3876.4,247 3968,242.82 5436.5,246.83 5526.4,229 5556.1,223.1 5587.9,210.33 5611.9,\ +199.18", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="4168.4,178", + pos="5830.4,178", width=2.1123]; "variant to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="4158.4,221.5", - pos="e,4139.6,194.78 2963.1,251.73 2987.8,249.87 3013.4,248.18 3037.4,247 3149.7,241.48 3939.4,252.2 4049.4,229 4077.7,223.03 4107.8,\ -210.35 4130.6,199.25", + lp="5823.4,221.5", + pos="e,5802.9,194.85 3800.9,251.66 3826,249.78 3852,248.1 3876.4,247 3978.5,242.39 5616.4,250.47 5716.4,229 5743.6,223.16 5772.2,210.57 \ +5794,199.48", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="4298.4,178", + pos="5960.4,178", width=1.011]; "variant to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="4306.9,221.5", - pos="e,4281.7,194.27 2962.5,251.72 2987.4,249.85 3013.2,248.16 3037.4,247 3103.2,243.85 4160.5,248.57 4223.4,229 4241.8,223.26 4259.9,\ -211.44 4273.7,200.73", + lp="5969.9,221.5", + pos="e,5944.5,194.3 3800.9,251.64 3826,249.76 3852,248.09 3876.4,247 3932.2,244.5 5835.1,245.94 5888.4,229 5906.3,223.31 5923.7,211.49 \ +5936.9,200.77", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="4426.4,178", + pos="6088.4,178", width=2.0401]; "variant to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="4434.4,221.5", - pos="e,4411.1,195.71 2962.5,251.69 2987.4,249.82 3013.2,248.14 3037.4,247 3110.9,243.54 4293,253.44 4362.4,229 4377.8,223.56 4392.5,212.76 \ -4403.8,202.58", + lp="6096.4,221.5", + pos="e,6073.2,195.99 3800.7,251.65 3825.8,249.77 3851.9,248.09 3876.4,247 3936,244.35 5969.1,248.89 6025.4,229 6040.4,223.68 6054.6,213.15 \ +6065.7,203.12", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="4562.4,178", + pos="6224.4,178", width=1.2277]; "variant to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="4550.4,221.5", - pos="e,4544.1,194.54 2962.2,251.69 2987.2,249.81 3013.1,248.13 3037.4,247 3117.6,243.27 4405.4,251.61 4482.4,229 4501.8,223.29 4521.2,\ -211.42 4536,200.68", + lp="6212.4,221.5", + pos="e,6206.1,194.57 3800.7,251.64 3825.8,249.76 3851.9,248.08 3876.4,247 3939.3,244.22 6083.9,246.61 6144.4,229 6163.9,223.34 6183.2,\ +211.47 6198,200.72", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="4668.4,178", + pos="6330.4,178", width=1.2277]; "variant to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="4653.9,221.5", - pos="e,4650.4,194.55 2962.2,251.67 2987.2,249.8 3013.1,248.12 3037.4,247 3123.5,243.04 4506.7,253.49 4589.4,229 4608.6,223.3 4627.7,211.43 \ -4642.3,200.69", + lp="6315.9,221.5", + pos="e,6312.4,194.57 3800.7,251.63 3825.8,249.75 3851.9,248.08 3876.4,247 3942.3,244.1 6188.1,247.61 6251.4,229 6270.7,223.34 6289.8,\ +211.47 6304.3,200.72", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="4772.4,178", + pos="6434.4,178", width=1.1735]; "variant to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="4768.4,221.5", - pos="e,4753.7,194.32 2961.9,251.68 2987,249.8 3013,248.12 3037.4,247 3129.1,242.81 4601.1,254.06 4689.4,229 4709.6,223.28 4729.7,211.29 \ -4745.2,200.48", + lp="6430.4,221.5", + pos="e,6415.7,194.34 3800.7,251.63 3825.8,249.75 3851.9,248.07 3876.4,247 3945.1,243.99 6285.2,247.65 6351.4,229 6371.6,223.32 6391.8,\ +211.33 6407.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4879.4,178", + pos="6541.4,178", width=1.1735]; "variant to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="4898.4,221.5", - pos="e,4864.9,195.48 2961.9,251.66 2987,249.78 3013,248.11 3037.4,247 3086.8,244.76 4770.9,245.69 4817.4,229 4832.5,223.59 4846.6,212.83 \ -4857.6,202.68", + lp="6560.4,221.5", + pos="e,6527.4,195 3800.7,251.62 3825.8,249.74 3851.9,248.07 3876.4,247 3948.6,243.84 6411.3,253.3 6479.4,229 6494.7,223.54 6509,212.56 \ +6520,202.28", style=solid]; relation [height=0.5, - pos="3793.4,18", + pos="5455.4,18", width=1.2999]; - object -> relation [pos="e,3781.9,35.705 3756,73.174 3762,64.509 3769.4,53.768 3776,44.141", + object -> relation [pos="e,5443.9,35.705 5418,73.174 5424,64.509 5431.4,53.768 5438,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3084.4,265", + pos="3923.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3215.4,265", + pos="4054.4,265", width=2.0762]; subject -> object [label=relation, - lp="3800.4,134.5", - pos="e,3750.8,108.97 3809.9,165.59 3797.1,159.94 3783,152.13 3772.4,142 3765.4,135.31 3759.7,126.48 3755.3,118.1"]; - subject -> relation [pos="e,3804.6,35.828 3841,159.99 3838.9,139.02 3834,102.55 3823.4,73 3819.9,63.258 3814.8,53.189 3809.8,44.423", + lp="5462.4,134.5", + pos="e,5412.8,108.97 5471.9,165.59 5459.1,159.94 5445,152.13 5434.4,142 5427.4,135.31 5421.7,126.48 5417.3,118.1"]; + subject -> relation [pos="e,5466.6,35.828 5503,159.99 5500.9,139.02 5496,102.55 5485.4,73 5481.9,63.258 5476.8,53.189 5471.8,44.423", style=dotted]; "variant to phenotypic feature association_subject" [color=blue, height=0.5, label="sequence variant", - pos="3398.4,265", + pos="4237.4,265", width=2.5095]; } diff --git a/graphviz/variant_to_phenotypic_feature_association.svg b/graphviz/variant_to_phenotypic_feature_association.svg index 15e84ba2ca..5ab032189a 100644 --- a/graphviz/variant_to_phenotypic_feature_association.svg +++ b/graphviz/variant_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to phenotypic feature association - -variant to phenotypic feature association + +variant to phenotypic feature association @@ -24,9 +24,9 @@ variant to phenotypic feature association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ variant to phenotypic feature association->variant to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to phenotypic feature association->entity to phenotypic feature association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ variant to phenotypic feature association->id - - -id + + +id @@ -76,8 +76,8 @@ variant to phenotypic feature association->iri - - + + iri @@ -89,8 +89,8 @@ variant to phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ variant to phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ variant to phenotypic feature association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ variant to phenotypic feature association->predicate - - + + predicate object - -named thing + +named thing variant to phenotypic feature association->object - - + + object @@ -154,8 +154,8 @@ variant to phenotypic feature association->negated - - + + negated @@ -167,9 +167,9 @@ variant to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ variant to phenotypic feature association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ variant to phenotypic feature association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ variant to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ variant to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ variant to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ variant to phenotypic feature association->timepoint - - -timepoint + + +timepoint @@ -258,9 +258,9 @@ variant to phenotypic feature association->original subject - - -original subject + + +original subject @@ -271,9 +271,9 @@ variant to phenotypic feature association->original predicate - - -original predicate + + +original predicate @@ -284,195 +284,338 @@ variant to phenotypic feature association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +variant to phenotypic feature association->subject category + + +subject category + + + +object category + +ontology class + + + +variant to phenotypic feature association->object category + + +object category + + + +subject closure + +string + + + +variant to phenotypic feature association->subject closure + + +subject closure + + + +object closure + +string + + + +variant to phenotypic feature association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +variant to phenotypic feature association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +variant to phenotypic feature association->object category closure + + +object category closure + + + +subject namespace + +string + + + +variant to phenotypic feature association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +variant to phenotypic feature association->object namespace + + +object namespace + + + +subject label closure + +string + + + +variant to phenotypic feature association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +variant to phenotypic feature association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +variant to phenotypic feature association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + variant to phenotypic feature association->type - - -type + + +type - + category - -category + +category - + variant to phenotypic feature association->category - - -category + + +category - + subject - -subject + +subject - + variant to phenotypic feature association->subject - - -subject + + +subject - + frequency qualifier - -frequency value + +frequency value - + variant to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + variant to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + variant to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier - + sex qualifier - -biological sex + +biological sex - + variant to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier - + has count - -integer + +integer - + variant to phenotypic feature association->has count - - -has count + + +has count - + has total - -integer + +integer - + variant to phenotypic feature association->has total - - -has total + + +has total - + has quotient - -double + +double - + variant to phenotypic feature association->has quotient - - -has quotient + + +has quotient - + has percentage - -double + +double - + variant to phenotypic feature association->has percentage - - -has percentage + + +has percentage - + relation - -relation + +relation - + object->relation - - + + - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + subject->relation - - + + - + variant to phenotypic feature association_subject - -sequence variant + +sequence variant diff --git a/graphviz/variant_to_population_association.gv b/graphviz/variant_to_population_association.gv index 0d9ed50ba9..7601a82b31 100644 --- a/graphviz/variant_to_population_association.gv +++ b/graphviz/variant_to_population_association.gv @@ -1,35 +1,35 @@ digraph { - graph [bb="0,0,4618.5,283"]; + graph [bb="0,0,6331.5,283"]; node [label="\N"]; "variant to population association" [height=0.5, label="variant to population association", - pos="2584.4,265", + pos="3494.4,265", width=4.5315]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to population association" -> association [label=is_a, - lp="611.39,221.5", - pos="e,106.49,190.74 2421.4,264.07 2081.9,263.57 1274.3,259.01 597.39,229 390.85,219.84 337.72,227.51 133.39,196 127.91,195.15 122.23,\ -194.1 116.58,192.94"]; + lp="608.39,221.5", + pos="e,106.49,190.74 3331.6,263.31 2802.4,260.87 1133.5,251.53 594.39,229 389.16,220.42 336.4,227.35 133.39,196 127.91,195.15 122.23,\ +194.1 116.58,192.93"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to population association" -> "variant to entity association mixin" [label=uses, - lp="821.89,221.5", - pos="e,417.5,192.16 2422.6,262.5 2045.6,258.75 1117,247.84 805.39,229 675.67,221.16 527.38,205.16 427.61,193.36"]; + lp="816.89,221.5", + pos="e,415.94,192.31 3331.3,263.79 2827.1,262.84 1296.8,257.6 800.39,229 671.75,221.59 524.7,205.47 425.95,193.53"]; "frequency quantifier" [height=0.5, pos="605.39,178", width=2.9247]; "variant to population association" -> "frequency quantifier" [label=uses, - lp="1006.9,221.5", - pos="e,678.59,191.05 2422.7,262.5 2074.9,258.93 1264.9,248.74 990.39,229 886,221.49 766.61,204.7 688.81,192.64"]; + lp="998.89,221.5", + pos="e,677.05,191.21 3331.4,264.1 2850.3,264.03 1441.4,261.01 982.39,229 880.12,221.87 763.21,204.99 687.05,192.82"]; "frequency qualifier mixin" [height=0.5, pos="856.39,178", width=3.5386]; "variant to population association" -> "frequency qualifier mixin" [label=uses, - lp="1138.9,221.5", - pos="e,918.85,193.7 2421.6,263.42 2094.9,261.72 1369.8,255.04 1122.4,229 1056.3,222.05 982.09,207.52 928.87,195.91"]; + lp="1137.9,221.5", + pos="e,918.07,193.75 3331.9,263.22 2832.2,260.6 1339.3,251 1121.4,229 1055.3,222.33 981.1,207.7 928.05,195.98"]; id [color=blue, height=0.5, label=string, @@ -37,9 +37,9 @@ digraph { width=1.0652]; "variant to population association" -> id [color=blue, label=id, - lp="1260.4,221.5", - pos="e,1069.4,190.01 2421.9,263.2 2118.2,261.14 1474.9,253.88 1253.4,229 1179.1,220.65 1160.5,215.87 1088.4,196 1085.3,195.14 1082.1,\ -194.18 1078.9,193.17", + lp="1257.4,221.5", + pos="e,1069.4,190 3331.8,263.21 2850.8,260.61 1455,251.24 1250.4,229 1177.3,221.06 1159.2,215.65 1088.4,196 1085.3,195.14 1082.1,194.17 \ +1078.9,193.16", style=solid]; iri [color=blue, height=0.5, @@ -48,9 +48,9 @@ digraph { width=1.2277]; "variant to population association" -> iri [color=blue, label=iri, - lp="1380.4,221.5", - pos="e,1174,190.18 2422.8,262.43 2141,259.17 1571,250.15 1372.4,229 1292.4,220.48 1272.4,215.66 1194.4,196 1191,195.14 1187.4,194.17 \ -1183.9,193.15", + lp="1374.4,221.5", + pos="e,1174.3,190.23 3332.1,262.95 2868.5,259.73 1559.4,248.95 1366.4,229 1289,221 1269.8,215.26 1194.4,196 1191,195.14 1187.5,194.18 \ +1184,193.17", style=solid]; name [color=blue, height=0.5, @@ -59,8 +59,8 @@ digraph { width=1.5707]; "variant to population association" -> name [color=blue, label=name, - lp="1495.4,221.5", - pos="e,1300.4,190.92 2422.7,262.6 2160.4,259.71 1653.6,251.34 1475.4,229 1417.9,221.79 1353.3,205.65 1310.1,193.65", + lp="1485.4,221.5", + pos="e,1299.2,191.28 3332,263.21 2883.3,260.76 1647.9,251.97 1465.4,229 1411,222.16 1350.1,206.23 1309,194.17", style=solid]; description [color=blue, height=0.5, @@ -69,8 +69,8 @@ digraph { width=2.0943]; "variant to population association" -> description [color=blue, label=description, - lp="1621.9,221.5", - pos="e,1449.5,193.47 2421.7,263.24 2180.1,261.28 1738.1,254.24 1581.4,229 1539.3,222.22 1492.9,208.24 1459.1,196.78", + lp="1612.9,221.5", + pos="e,1447.6,193.79 3331.6,263.65 2899.2,262.36 1743.3,256.37 1572.4,229 1532.6,222.63 1489.1,208.78 1457.2,197.27", style=solid]; "has attribute" [color=blue, height=0.5, @@ -79,8 +79,8 @@ digraph { width=1.4443]; "variant to population association" -> "has attribute" [color=blue, label="has attribute", - lp="1776.4,221.5", - pos="e,1589.8,191.55 2423.5,261.99 2213.7,258.58 1858.4,249.86 1729.4,229 1684.4,221.71 1634.4,206.61 1599.7,194.9", + lp="1769.4,221.5", + pos="e,1588.7,191.89 3331.9,263.3 2923.9,261.19 1878.4,253.43 1722.4,229 1679.1,222.22 1631.4,207.13 1598.1,195.29", style=solid]; predicate [color=blue, height=0.5, @@ -89,8 +89,8 @@ digraph { width=2.1665]; "variant to population association" -> predicate [color=blue, label=predicate, - lp="1930.4,221.5", - pos="e,1746.9,192.99 2428.2,259.73 2257.4,254.4 1995,244.13 1896.4,229 1848.5,221.66 1795.3,207.39 1756.9,195.97", + lp="1928.4,221.5", + pos="e,1746,193.24 3332.6,262.61 2954.3,259.05 2033.7,248.49 1894.4,229 1846.7,222.33 1793.9,207.93 1755.9,196.29", style=solid]; negated [color=blue, height=0.5, @@ -99,8 +99,8 @@ digraph { width=1.2999]; "variant to population association" -> negated [color=blue, label=negated, - lp="2066.4,221.5", - pos="e,1880.8,190.35 2425,261.11 2315.5,257.35 2167,248.71 2037.4,229 1986.2,221.22 1929,205.22 1890.6,193.4", + lp="2071.4,221.5", + pos="e,1880.6,190.46 3331.3,264.29 3006.1,264.18 2287.1,260.25 2042.4,229 1989.1,222.19 1929.5,205.66 1890.1,193.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -109,8 +109,8 @@ digraph { width=2.1304]; "variant to population association" -> qualifiers [color=blue, label=qualifiers, - lp="2194.9,221.5", - pos="e,2028.3,193.25 2431.7,258.64 2350.9,253.98 2250.2,245.27 2161.4,229 2119.2,221.27 2072.5,207.56 2038.1,196.45", + lp="2210.9,221.5", + pos="e,2029.5,193.07 3331.1,264.36 3029.4,264.24 2395.2,260.12 2177.4,229 2129.8,222.2 2077.1,207.74 2039.2,196.11", style=solid]; publications [color=blue, height=0.5, @@ -119,8 +119,8 @@ digraph { width=1.7332]; "variant to population association" -> publications [color=blue, label=publications, - lp="2326.4,221.5", - pos="e,2177.2,193.34 2448.3,254.99 2396,249.77 2336,241.62 2282.4,229 2249.5,221.24 2213.6,208.09 2186.7,197.22", + lp="2358.4,221.5", + pos="e,2180.9,192.71 3331.3,264.32 3054.8,263.99 2505.2,259.37 2314.4,229 2271.5,222.18 2224.3,207.69 2190.5,196.06", style=solid]; "has evidence" [color=blue, height=0.5, @@ -129,8 +129,8 @@ digraph { width=2.0943]; "variant to population association" -> "has evidence" [color=blue, label="has evidence", - lp="2457.9,221.5", - pos="e,2330.3,194.68 2495,249.86 2467.8,244.51 2438.1,237.59 2411.4,229 2386.8,221.08 2360.4,209.32 2339.5,199.19", + lp="2512.9,221.5", + pos="e,2338.6,193.61 3331.6,263.57 3084.9,262.05 2627.8,255.6 2466.4,229 2425.8,222.3 2381.1,208.48 2348.4,197.06", style=solid]; "knowledge source" [color=blue, height=0.5, @@ -139,8 +139,8 @@ digraph { width=3.015]; "variant to population association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2580.9,221.5", - pos="e,2503.8,196.34 2539.6,247.63 2530.9,242.75 2522.6,236.61 2516.4,229 2511.1,222.52 2507.8,214.16 2505.8,206.15", + lp="2667.9,221.5", + pos="e,2528.2,195.59 3334.6,261.34 3097.3,256.84 2672,246.47 2603.4,229 2580.1,223.06 2555.9,211.3 2537,200.68", style=solid]; "primary knowledge source" [color=blue, height=0.5, @@ -149,9 +149,8 @@ digraph { width=3.015]; "variant to population association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2763.4,221.5", - pos="e,2703.7,195.19 2614.4,247.25 2624.3,241.57 2635.4,235.12 2645.4,229 2655.8,222.63 2657.8,220.1 2668.4,214 2676.8,209.16 2685.9,\ -204.28 2694.7,199.76", + lp="2839.4,221.5", + pos="e,2734.8,196.37 3333.9,261.67 3120.1,257.83 2765.8,248.54 2744.4,229 2738.2,223.35 2735.7,214.95 2734.9,206.63", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, @@ -160,9 +159,8 @@ digraph { width=3.015]; "variant to population association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2987.9,221.5", - pos="e,2926.7,194.43 2697.4,251.98 2765.9,244.26 2843,234.66 2858.4,229 2869.8,224.79 2870.5,219.55 2881.4,214 2892.7,208.22 2905.2,202.83 \ -2917.2,198.09", + lp="3047.9,221.5", + pos="e,2951.1,195.91 3331.3,264.77 3177.8,263.73 2967.8,257.1 2941.4,229 2934.3,221.47 2937.7,212.1 2944.3,203.51", style=solid]; timepoint [color=blue, height=0.5, @@ -171,9 +169,8 @@ digraph { width=1.5346]; "variant to population association" -> timepoint [color=blue, label=timepoint, - lp="3151.4,221.5", - pos="e,3137.5,195.19 2698.1,252.02 2717.6,250.19 2737.5,248.43 2756.4,247 2831.4,241.3 3024.4,256.48 3094.4,229 3102.3,225.88 3117,213.74 \ -3129.8,202.21", + lp="3202.4,221.5", + pos="e,3154.2,196.41 3351.8,256.21 3270.5,250.46 3181.9,241.47 3167.4,229 3160.8,223.34 3157.4,214.82 3155.6,206.41", style=solid]; "original subject" [color=blue, height=0.5, @@ -182,9 +179,8 @@ digraph { width=1.0652]; "variant to population association" -> "original subject" [color=blue, label="original subject", - lp="3266.4,221.5", - pos="e,3244.3,192.7 2697.2,251.93 2716.9,250.08 2737.2,248.35 2756.4,247 2852,240.28 3096.1,258.23 3187.4,229 3199,225.28 3200.1,220.57 \ -3210.4,214 3218.6,208.79 3227.4,203.21 3235.7,198.07", + lp="3300.4,221.5", + pos="e,3251.2,194.78 3341,258.83 3297.6,253.95 3258.3,245.04 3244.4,229 3238,221.59 3240.3,212 3245.4,203.21", style=solid]; "original predicate" [color=blue, height=0.5, @@ -193,9 +189,8 @@ digraph { width=1.5887]; "variant to population association" -> "original predicate" [color=blue, label="original predicate", - lp="3407.9,221.5", - pos="e,3363.8,195.49 2696.3,251.85 2716.3,249.99 2736.9,248.27 2756.4,247 2819.2,242.9 3263.8,251.85 3322.4,229 3330.1,225.98 3344.2,\ -213.98 3356.5,202.5", + lp="3426.9,221.5", + pos="e,3367.4,195.6 3409.1,249.62 3388.2,244.3 3369.9,237.45 3363.4,229 3358,221.92 3359.1,212.99 3362.6,204.65", style=solid]; "original object" [color=blue, height=0.5, @@ -204,138 +199,256 @@ digraph { width=1.0652]; "variant to population association" -> "original object" [color=blue, label="original object", - lp="3536.9,221.5", - pos="e,3491.6,196.43 2695.8,251.79 2715.9,249.92 2736.8,248.21 2756.4,247 2796.1,244.54 3439.3,251.16 3472.4,229 3480.3,223.7 3485.4,\ -214.89 3488.6,206.12", + lp="3545.9,221.5", + pos="e,3494.4,196.18 3494.4,246.8 3494.4,235.16 3494.4,219.55 3494.4,206.24", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3627.4,178", + width=2.1304]; + "variant to population association" -> "subject category" [color=blue, + label="subject category", + lp="3670.9,221.5", + pos="e,3621.2,195.97 3563.2,248.67 3575.8,243.78 3588.1,237.38 3598.4,229 3606.2,222.66 3612.3,213.66 3616.9,205.03", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3798.4,178", + width=2.1304]; + "variant to population association" -> "object category" [color=blue, + label="object category", + lp="3814.9,221.5", + pos="e,3782.1,195.71 3612.4,252.51 3661.4,246.55 3712.1,238.52 3734.4,229 3749,222.76 3763.1,212.32 3774.4,202.6", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3931.4,178", + width=1.0652]; + "variant to population association" -> "subject closure" [color=blue, + label="subject closure", + lp="3948.9,221.5", + pos="e,3915.9,194.59 3610.5,252.33 3629.2,250.51 3648.3,248.68 3666.4,247 3712.6,242.72 3831.7,247.2 3874.4,229 3882.1,225.71 3896.3,\ +213.29 3908.6,201.65", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="4027.4,178", + width=1.0652]; + "variant to population association" -> "object closure" [color=blue, + label="object closure", + lp="4068.4,221.5", + pos="e,4024.9,196.31 3608.1,252.02 3627.6,250.19 3647.5,248.43 3666.4,247 3704.1,244.14 3975.5,250.77 4006.4,229 4014.1,223.57 4019,214.72 \ +4022.1,205.97", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4160.4,178", + width=2.1304]; + "variant to population association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="4226.9,221.5", + pos="e,4152.4,196.15 3606.7,251.93 3626.6,250.08 3647.1,248.33 3666.4,247 3717,243.5 4077.4,252.42 4122.4,229 4132.7,223.66 4140.9,214.15 \ +4147.1,204.86", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="4349.4,178", + width=2.1304]; + "variant to population association" -> "object category closure" [color=blue, + label="object category closure", + lp="4416.9,221.5", + pos="e,4343.7,196.11 3605.8,251.83 3625.9,249.96 3646.8,248.24 3666.4,247 3702.6,244.72 4287,247.06 4318.4,229 4327.6,223.71 4334.4,214.48 \ +4339.3,205.37", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4539.4,178", + width=1.0652]; + "variant to population association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4589.4,221.5", + pos="e,4532.4,196.19 3605.3,251.77 3625.6,249.89 3646.6,248.19 3666.4,247 3712.9,244.21 4463.3,250.95 4504.4,229 4514.2,223.76 4521.9,\ +214.4 4527.5,205.19", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4698.4,178", + width=1.0652]; + "variant to population association" -> "object namespace" [color=blue, + label="object namespace", + lp="4742.4,221.5", + pos="e,4691,195.74 3605.3,251.71 3625.6,249.84 3646.6,248.15 3666.4,247 3721.6,243.78 4612.3,254.33 4661.4,229 4671.7,223.68 4679.9,213.99 \ +4685.9,204.56", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4849.4,178", + width=1.0652]; + "variant to population association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4902.4,221.5", + pos="e,4841.4,195.77 3604.9,251.72 3625.3,249.83 3646.5,248.14 3666.4,247 3698.1,245.19 4781.9,243.17 4810.4,229 4821.1,223.66 4829.8,\ +213.84 4836.2,204.31", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="5020.4,178", + width=1.0652]; + "variant to population association" -> "object label closure" [color=blue, + label="object label closure", + lp="5067.9,221.5", + pos="e,5012.1,195.79 3604.9,251.68 3625.3,249.8 3646.5,248.12 3666.4,247 3702.8,244.95 4947.6,245.04 4980.4,229 4991.3,223.69 5000.1,\ +213.87 5006.7,204.33", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="5161.4,178", + width=2.347]; + "variant to population association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="5222.9,221.5", + pos="e,5159.3,196.42 3604.4,251.7 3625,249.81 3646.3,248.11 3666.4,247 3707.3,244.73 5107.6,252.18 5141.4,229 5149.1,223.7 5153.9,214.88 \ +5156.8,206.11", style=solid]; type [height=0.5, - pos="3582.4,178", + pos="5295.4,178", width=0.86659]; "variant to population association" -> type [color=blue, label=type, - lp="3614.4,221.5", - pos="e,3592.3,195.51 2695.3,251.77 2715.6,249.89 2736.6,248.19 2756.4,247 2779.6,245.61 3576.1,245.6 3592.4,229 3598.6,222.66 3598.4,\ -213.61 3595.9,204.96", + lp="5319.4,221.5", + pos="e,5301.3,196.13 3604.4,251.68 3625,249.79 3646.3,248.1 3666.4,247 3689,245.76 5280.5,245.1 5296.4,229 5302.3,223.03 5303.6,214.44 \ +5302.9,206.06", style=solid]; category [height=0.5, - pos="3683.4,178", + pos="5396.4,178", width=1.4263]; "variant to population association" -> category [color=blue, label=category, - lp="3687.9,221.5", - pos="e,3672.3,195.84 2695.3,251.75 2715.6,249.88 2736.6,248.18 2756.4,247 2805.1,244.1 3589.6,248.36 3634.4,229 3646.8,223.65 3657.6,\ -213.55 3665.9,203.82", + lp="5395.9,221.5", + pos="e,5383.4,195.45 3604.4,251.68 3625,249.79 3646.3,248.1 3666.4,247 3712.8,244.46 5296,245.61 5339.4,229 5353.5,223.6 5366.4,213 5376.4,\ +202.94", style=solid]; subject [height=0.5, - pos="3797.4,178", + pos="5510.4,178", width=1.2277]; "variant to population association" -> subject [color=blue, label=subject, - lp="3780.4,221.5", - pos="e,3780.4,194.74 2695.3,251.72 2715.6,249.85 2736.6,248.16 2756.4,247 2810,243.86 3672.2,245.21 3723.4,229 3741.4,223.31 3759,211.72 \ -3772.5,201.14", + lp="5490.4,221.5", + pos="e,5492.4,194.55 3604.4,251.67 3625,249.78 3646.3,248.09 3666.4,247 3764.3,241.67 5337.4,256.78 5431.4,229 5450.7,223.31 5469.7,211.44 \ +5484.3,200.7", style=solid]; object [height=0.5, - pos="3840.4,91", + pos="5553.4,91", width=1.0832]; "variant to population association" -> object [color=blue, label=object, - lp="3883.4,178", - pos="e,3853.8,108.09 2694.9,251.74 2715.3,249.85 2736.5,248.15 2756.4,247 2814.9,243.62 3755.5,249.27 3810.4,229 3852.9,213.33 3858.1,\ -186.96 3863.4,142 3864.2,135.38 3865.3,133.39 3863.4,127 3862.4,123.55 3860.9,120.13 3859.1,116.85", + lp="5597.4,178", + pos="e,5566.8,108.09 3604.4,251.66 3625,249.77 3646.3,248.09 3666.4,247 3717.8,244.21 5471.7,245.79 5520.4,229 5543.2,221.14 5550.3,216.2 \ +5563.4,196 5576.8,175.3 5573.5,166.51 5576.4,142 5577.2,135.38 5578.3,133.39 5576.4,127 5575.4,123.55 5573.9,120.13 5572.1,116.85", style=solid]; "has quotient" [height=0.5, - pos="4008.4,178", + pos="5721.4,178", width=1.9137]; "variant to population association" -> "has quotient" [color=blue, label="has quotient", - lp="3983.4,221.5", - pos="e,3980.6,194.55 2694.9,251.72 2715.3,249.84 2736.5,248.14 2756.4,247 2882.3,239.79 3768,255.27 3891.4,229 3919.4,223.04 3949,210.32 \ -3971.4,199.2", + lp="5696.4,221.5", + pos="e,5693.6,194.61 3604.4,251.65 3625,249.76 3646.3,248.08 3666.4,247 3773.9,241.2 5499,251.08 5604.4,229 5632.4,223.13 5662,210.41 \ +5684.4,199.26", style=solid]; "has count" [height=0.5, - pos="4151.4,178", + pos="5864.4,178", width=1.5526]; "variant to population association" -> "has count" [color=blue, label="has count", - lp="4115.4,221.5", - pos="e,4124.5,193.84 2694.9,251.69 2715.3,249.81 2736.5,248.12 2756.4,247 2898,239.02 3893.6,257.99 4032.4,229 4061.5,222.92 4092.4,209.7 \ -4115.4,198.39", + lp="5828.4,221.5", + pos="e,5837.5,193.89 3604.4,251.64 3625,249.75 3646.3,248.08 3666.4,247 3781.7,240.81 5632.3,252.31 5745.4,229 5774.5,223 5805.4,209.78 \ +5828.4,198.44", style=solid]; "has total" [height=0.5, - pos="4276.4,178", + pos="5989.4,178", width=1.4263]; "variant to population association" -> "has total" [color=blue, label="has total", - lp="4234.9,221.5", - pos="e,4249.2,193.61 2694.9,251.67 2715.3,249.79 2736.5,248.11 2756.4,247 2911.5,238.35 4002.2,260 4154.4,229 4184.4,222.9 4216.3,209.55 \ -4239.9,198.18", + lp="5947.9,221.5", + pos="e,5962.7,193.41 3604.4,251.64 3625,249.75 3646.3,248.07 3666.4,247 3788.5,240.48 5747.5,253.12 5867.4,229 5897.7,222.9 5930,209.32 \ +5953.7,197.85", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="4388.4,178", + pos="6101.4,178", width=1.1735]; "variant to population association" -> "has percentage" [color=blue, label="has percentage", - lp="4372.4,221.5", - pos="e,4363.5,192.91 2694.4,251.7 2715,249.8 2736.3,248.11 2756.4,247 2840.4,242.36 4188.1,246.23 4270.4,229 4300.1,222.79 4331.6,209.03 \ -4354.6,197.51", + lp="6085.4,221.5", + pos="e,6077,192.7 3604.4,251.63 3625,249.74 3646.3,248.07 3666.4,247 3794.9,240.16 5857.3,255.11 5983.4,229 6013.3,222.81 6045,208.91 \ +6068,197.33", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="4533.4,178", + pos="6246.4,178", width=2.3651]; "variant to population association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="4539.4,221.5", - pos="e,4508.2,195.32 2694.4,251.68 2715,249.79 2736.3,248.1 2756.4,247 2849.3,241.92 4340.9,250.51 4431.4,229 4455.4,223.29 4480.3,211.21 \ -4499.5,200.36", + lp="6252.4,221.5", + pos="e,6221.2,195.35 3604.4,251.62 3625,249.73 3646.3,248.06 3666.4,247 3735.1,243.36 6077.4,244.79 6144.4,229 6168.4,223.34 6193.3,211.26 \ +6212.5,200.39", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2803.4,265", + pos="3713.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2934.4,265", + pos="3844.4,265", width=2.0762]; subject -> object [label=relation, - lp="3835.4,134.5", - pos="e,3822.5,107.23 3798.5,159.55 3799.7,149.57 3802.2,137.07 3807.4,127 3809.6,122.68 3812.5,118.52 3815.7,114.66"]; + lp="5548.4,134.5", + pos="e,5535.5,107.23 5511.5,159.55 5512.7,149.57 5515.2,137.07 5520.4,127 5522.6,122.68 5525.5,118.52 5528.7,114.66"]; relation [height=0.5, - pos="3785.4,18", + pos="5498.4,18", width=1.2999]; - subject -> relation [pos="e,3786.7,36.188 3796.1,159.79 3794,132.48 3790,78.994 3787.5,46.38", + subject -> relation [pos="e,5499.7,36.188 5509.1,159.79 5507,132.48 5503,78.994 5500.5,46.38", style=dotted]; "variant to population association_subject" [color=blue, height=0.5, label="sequence variant", - pos="3117.4,265", + pos="4027.4,265", width=2.5095]; - object -> relation [pos="e,3798.2,35.54 3827.9,73.889 3821,64.939 3812.2,53.617 3804.4,43.584", + object -> relation [pos="e,5511.2,35.54 5540.9,73.889 5534,64.939 5525.2,53.617 5517.4,43.584", style=dotted]; "variant to population association_object" [color=blue, height=0.5, label="population of individual organisms", - pos="3397.4,265", + pos="4307.4,265", width=4.7662]; "variant to population association_has quotient" [color=blue, height=0.5, label=double, - pos="3629.4,265", + pos="4539.4,265", width=1.1735]; "variant to population association_has count" [color=blue, height=0.5, label=integer, - pos="3733.4,265", + pos="4643.4,265", width=1.2277]; "variant to population association_has total" [color=blue, height=0.5, label=integer, - pos="3839.4,265", + pos="4749.4,265", width=1.2277]; } diff --git a/graphviz/variant_to_population_association.svg b/graphviz/variant_to_population_association.svg index 5e43efef75..27580d1ca1 100644 --- a/graphviz/variant_to_population_association.svg +++ b/graphviz/variant_to_population_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to population association - -variant to population association + +variant to population association @@ -24,9 +24,9 @@ variant to population association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ variant to population association->variant to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to population association->frequency quantifier - - -uses + + +uses @@ -63,9 +63,9 @@ variant to population association->frequency qualifier mixin - - -uses + + +uses @@ -76,9 +76,9 @@ variant to population association->id - - -id + + +id @@ -89,9 +89,9 @@ variant to population association->iri - - -iri + + +iri @@ -102,9 +102,9 @@ variant to population association->name - - -name + + +name @@ -115,9 +115,9 @@ variant to population association->description - - -description + + +description @@ -128,9 +128,9 @@ variant to population association->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ variant to population association->predicate - - -predicate + + +predicate @@ -154,9 +154,9 @@ variant to population association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ variant to population association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ variant to population association->publications - - -publications + + +publications @@ -193,9 +193,9 @@ variant to population association->has evidence - - -has evidence + + +has evidence @@ -206,9 +206,9 @@ variant to population association->knowledge source - - -knowledge source + + +knowledge source @@ -219,9 +219,9 @@ variant to population association->primary knowledge source - - -primary knowledge source + + +primary knowledge source @@ -232,9 +232,9 @@ variant to population association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source @@ -245,9 +245,9 @@ variant to population association->timepoint - - -timepoint + + +timepoint @@ -258,9 +258,9 @@ variant to population association->original subject - - -original subject + + +original subject @@ -271,9 +271,9 @@ variant to population association->original predicate - - -original predicate + + +original predicate @@ -284,193 +284,336 @@ variant to population association->original object - - -original object + + +original object - + +subject category + +ontology class + + + +variant to population association->subject category + + +subject category + + + +object category + +ontology class + + + +variant to population association->object category + + +object category + + + +subject closure + +string + + + +variant to population association->subject closure + + +subject closure + + + +object closure + +string + + + +variant to population association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +variant to population association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +variant to population association->object category closure + + +object category closure + + + +subject namespace + +string + + + +variant to population association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +variant to population association->object namespace + + +object namespace + + + +subject label closure + +string + + + +variant to population association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +variant to population association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +variant to population association->retrieval source ids + + +retrieval source ids + + + type - -type + +type - + variant to population association->type - - -type + + +type - + category - -category + +category - + variant to population association->category - - -category + + +category - + subject - -subject + +subject - + variant to population association->subject - - -subject + + +subject - + object - -object + +object - + variant to population association->object - - -object + + +object - + has quotient - -has quotient + +has quotient - + variant to population association->has quotient - - -has quotient + + +has quotient - + has count - -has count + +has count - + variant to population association->has count - - -has count + + +has count - + has total - -has total + +has total - + variant to population association->has total - - -has total + + +has total - + has percentage - -double + +double - + variant to population association->has percentage - - -has percentage + + +has percentage - + frequency qualifier - -frequency value + +frequency value - + variant to population association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + association_type - -string + +string - + association_category - -category type + +category type - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + variant to population association_subject - -sequence variant + +sequence variant - + object->relation - - + + - + variant to population association_object - -population of individual organisms + +population of individual organisms - + variant to population association_has quotient - -double + +double - + variant to population association_has count - -integer + +integer - + variant to population association_has total - -integer + +integer diff --git a/json-schema/biolink-model.json b/json-schema/biolink-model.json index 4c2deadc0d..16f748f616 100644 --- a/json-schema/biolink-model.json +++ b/json-schema/biolink-model.json @@ -1 +1 @@ -{"$defs": {"AccessibleDnaRegion": {"additionalProperties": false, "description": "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "AccessibleDnaRegion", "type": "object"}, "Activity": {"additionalProperties": false, "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "person, group, organization or project that provides a piece of information (i.e. a knowledge association)", "properties": {"address": {"description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", "type": "string"}, "affiliation": {"description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Agent", "type": "object"}, "AnatomicalContextQualifierEnum": {"description": "", "enum": [], "title": "AnatomicalContextQualifierEnum", "type": "string"}, "AnatomicalEntity": {"additionalProperties": false, "description": "A subcellular location, cell type or gross anatomical part", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "AnatomicalEntity", "type": "object"}, "AnatomicalEntityToAnatomicalEntityOntogenicAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the structure at an earlier time", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the structure at a later time", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityOntogenicAssociation", "type": "object"}, "AnatomicalEntityToAnatomicalEntityPartOfAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the whole", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the part", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityPartOfAssociation", "type": "object"}, "Article": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent serial containing the article should have industry-standard identifier from ISSN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category"], "title": "Article", "type": "object"}, "Association": {"additionalProperties": false, "description": "A typed association between two entities, supported by evidence", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "Association", "type": "object"}, "Attribute": {"additionalProperties": false, "description": "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Attribute", "type": "object"}, "Behavior": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Behavior", "type": "object"}, "BehaviorToBehavioralFeatureAssociation": {"additionalProperties": false, "description": "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "behavioral feature that is the object of the association", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "behavior that is the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "BehaviorToBehavioralFeatureAssociation", "type": "object"}, "BehavioralExposure": {"additionalProperties": false, "description": "A behavioral exposure is a factor relating to behavior impacting an individual.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BehavioralExposure", "type": "object"}, "BehavioralFeature": {"additionalProperties": false, "description": "A phenotypic feature which is behavioral in nature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BehavioralFeature", "type": "object"}, "BehavioralOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of human behavior.", "title": "BehavioralOutcome", "type": "object"}, "BiologicalProcess": {"additionalProperties": false, "description": "One or more causally connected executions of molecular functions", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcess", "type": "object"}, "BiologicalProcessOrActivity": {"additionalProperties": false, "description": "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcessOrActivity", "type": "object"}, "BiologicalSex": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BiologicalSex", "type": "object"}, "BioticExposure": {"additionalProperties": false, "description": "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BioticExposure", "type": "object"}, "Book": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Books should have industry-standard identifier such as from ISBN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'book'.", "items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Book", "type": "object"}, "BookChapter": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "chapter": {"description": "chapter of a book", "type": "string"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category"], "title": "BookChapter", "type": "object"}, "Case": {"additionalProperties": false, "description": "An individual (human) organism that has a patient role in some clinical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Case", "type": "object"}, "CaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "CaseToPhenotypicFeatureAssociation", "type": "object"}, "CausalMechanismQualifierEnum": {"description": "", "enum": ["binding", "inhibition", "antibody_inhibition", "antagonism", "molecular_channel_blockage", "inverse_agonism", "negative_allosteric_modulation", "agonism", "molecular_channel_opening", "positive_allosteric_modulation", "potentiation", "activation", "inducer", "transcriptional_regulation", "signaling_mediated_control", "stabilization", "stimulation", "releasing_activity"], "title": "CausalMechanismQualifierEnum", "type": "string"}, "Cell": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cell", "type": "object"}, "CellLine": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellLine", "type": "object"}, "CellLineAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineAsAModelOfDiseaseAssociation", "type": "object"}, "CellLineToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "CellularComponent": {"additionalProperties": false, "description": "A location in or around a cell", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularComponent", "type": "object"}, "CellularOrganism": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularOrganism", "type": "object"}, "ChemicalAffectsGeneAssociation": {"additionalProperties": false, "description": "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"$ref": "#/$defs/CausalMechanismQualifierEnum", "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalAffectsGeneAssociation", "type": "object"}, "ChemicalEntity": {"additionalProperties": false, "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalEntity", "type": "object"}, "ChemicalEntityAssessesNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityAssessesNamedThingAssociation", "type": "object"}, "ChemicalEntityDerivativeEnum": {"description": "", "enum": ["metabolite"], "title": "ChemicalEntityDerivativeEnum", "type": "string"}, "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation": {"additionalProperties": false, "description": "A regulatory relationship between two genes", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the direction is always from regulator to regulated", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation", "type": "object"}, "ChemicalExposure": {"additionalProperties": false, "description": "A chemical exposure is an intake of a particular chemical entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalExposure", "type": "object"}, "ChemicalGeneInteractionAssociation": {"additionalProperties": false, "description": "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalGeneInteractionAssociation", "type": "object"}, "ChemicalMixture": {"additionalProperties": false, "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalMixture", "type": "object"}, "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrGeneOrGeneProductFormOrVariantEnum": {"description": "", "enum": ["genetic_variant_form", "modified_form", "loss_of_function_variant_form", "gain_of_function_variant_form", "polymorphic_form", "snp_form", "analog_form"], "title": "ChemicalOrGeneOrGeneProductFormOrVariantEnum", "type": "string"}, "ChemicalRole": {"additionalProperties": false, "description": "A role played by the molecular entity or part thereof within a chemical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalRole", "type": "object"}, "ChemicalToChemicalAssociation": {"additionalProperties": false, "description": "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the chemical element that is the target of the statement", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalAssociation", "type": "object"}, "ChemicalToChemicalDerivationAssociation": {"additionalProperties": false, "description": "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "catalyst_qualifier": {"description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the downstream chemical entity", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the upstream chemical entity", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalDerivationAssociation", "type": "object"}, "ChemicalToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the disease or phenotype that is affected by the chemical", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that is affected by the chemical", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the chemical entity that is affecting the pathway", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToPathwayAssociation", "type": "object"}, "ChiSquaredAnalysisResult": {"additionalProperties": false, "description": "A result of a chi squared analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChiSquaredAnalysisResult", "type": "object"}, "ClinicalAttribute": {"additionalProperties": false, "description": "Attributes relating to a clinical manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalAttribute", "type": "object"}, "ClinicalCourse": {"additionalProperties": false, "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalCourse", "type": "object"}, "ClinicalEntity": {"additionalProperties": false, "description": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalEntity", "type": "object"}, "ClinicalFinding": {"additionalProperties": false, "description": "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalFinding", "type": "object"}, "ClinicalIntervention": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalIntervention", "type": "object"}, "ClinicalMeasurement": {"additionalProperties": false, "description": "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalMeasurement", "type": "object"}, "ClinicalModifier": {"additionalProperties": false, "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalModifier", "type": "object"}, "ClinicalTrial": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalTrial", "type": "object"}, "CodingSequence": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CodingSequence", "type": "object"}, "Cohort": {"additionalProperties": false, "description": "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cohort", "type": "object"}, "CommonDataElement": {"additionalProperties": false, "description": "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CommonDataElement", "type": "object"}, "ComplexChemicalExposure": {"additionalProperties": false, "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ComplexChemicalExposure", "type": "object"}, "ComplexMolecularMixture": {"additionalProperties": false, "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ComplexMolecularMixture", "type": "object"}, "ConceptCountAnalysisResult": {"additionalProperties": false, "description": "A result of a concept count analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConceptCountAnalysisResult", "type": "object"}, "ConfidenceLevel": {"additionalProperties": false, "description": "Level of confidence in a statement", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConfidenceLevel", "type": "object"}, "ContributorAssociation": {"additionalProperties": false, "description": "Any association between an entity (such as a publication) and various agents that contribute to its realisation", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "agent helping to realise the given entity (e.g. such as a publication)", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "information content entity which an agent has helped realise", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ContributorAssociation", "type": "object"}, "Dataset": {"additionalProperties": false, "description": "an item that refers to a collection of data from a data source.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Dataset", "type": "object"}, "DatasetDistribution": {"additionalProperties": false, "description": "an item that holds distribution level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "distribution_download_url": {"type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetDistribution", "type": "object"}, "DatasetSummary": {"additionalProperties": false, "description": "an item that holds summary level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "source_logo": {"type": "string"}, "source_web_page": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetSummary", "type": "object"}, "DatasetVersion": {"additionalProperties": false, "description": "an item that holds version level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_dataset": {"type": "string"}, "has_distribution": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "ingest_date": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetVersion", "type": "object"}, "Device": {"additionalProperties": false, "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Device", "type": "object"}, "DirectionQualifierEnum": {"description": "", "enum": ["increased", "upregulated", "decreased", "downregulated"], "title": "DirectionQualifierEnum", "type": "string"}, "Disease": {"additionalProperties": false, "description": "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Disease", "type": "object"}, "DiseaseOrPhenotypicFeature": {"additionalProperties": false, "description": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DiseaseOrPhenotypicFeature", "type": "object"}, "DiseaseOrPhenotypicFeatureExposure": {"additionalProperties": false, "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DiseaseOrPhenotypicFeatureExposure", "type": "object"}, "DiseaseOrPhenotypicFeatureOutcome": {"additionalProperties": false, "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.", "title": "DiseaseOrPhenotypicFeatureOutcome", "type": "object"}, "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "genetic inheritance associated with the specified disease or phenotypic feature.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "type": "object"}, "DiseaseOrPhenotypicFeatureToLocationAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "anatomical entity in which the disease or feature is found.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToLocationAssociation", "type": "object"}, "DiseaseToExposureEventAssociation": {"additionalProperties": false, "description": "An association between an exposure event and a disease.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToExposureEventAssociation", "type": "object"}, "DiseaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToPhenotypicFeatureAssociation", "type": "object"}, "Drug": {"additionalProperties": false, "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Drug", "type": "object"}, "DrugAvailabilityEnum": {"description": "", "enum": ["over_the_counter", "prescription"], "title": "DrugAvailabilityEnum", "type": "string"}, "DrugDeliveryEnum": {"description": "", "enum": ["inhalation", "oral", "absorption_through_the_skin", "intravenous_injection"], "title": "DrugDeliveryEnum", "type": "string"}, "DrugExposure": {"additionalProperties": false, "description": "A drug exposure is an intake of a particular drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugExposure", "type": "object"}, "DrugToGeneAssociation": {"additionalProperties": false, "description": "An interaction between a drug and a gene or gene product.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product that is affected by the drug"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DrugToGeneAssociation", "type": "object"}, "DrugToGeneInteractionExposure": {"additionalProperties": false, "description": "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugToGeneInteractionExposure", "type": "object"}, "DruggableGeneCategoryEnum": {"description": "", "enum": ["tclin", "tbio", "tchem", "tdark"], "title": "DruggableGeneCategoryEnum", "type": "string"}, "DruggableGeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"$ref": "#/$defs/DruggableGeneCategoryEnum"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DruggableGeneToDiseaseAssociation", "type": "object"}, "EntityToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToDiseaseAssociation", "type": "object"}, "EntityToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToPhenotypicFeatureAssociation", "type": "object"}, "EnvironmentalExposure": {"additionalProperties": false, "description": "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "EnvironmentalExposure", "type": "object"}, "EnvironmentalFeature": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFeature", "type": "object"}, "EnvironmentalFoodContaminant": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFoodContaminant", "type": "object"}, "EnvironmentalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalProcess", "type": "object"}, "EpidemiologicalOutcome": {"additionalProperties": false, "description": "An epidemiological outcome, such as societal disease burden, resulting from an exposure event.", "title": "EpidemiologicalOutcome", "type": "object"}, "Event": {"additionalProperties": false, "description": "Something that happens at a given place and time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Event", "type": "object"}, "EvidenceType": {"additionalProperties": false, "description": "Class of evidence that supports an association", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EvidenceType", "type": "object"}, "Exon": {"additionalProperties": false, "description": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Exon", "type": "object"}, "ExonToTranscriptRelationship": {"additionalProperties": false, "description": "A transcript is formed from multiple exons", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExonToTranscriptRelationship", "type": "object"}, "ExposureEventToOutcomeAssociation": {"additionalProperties": false, "description": "An association between an exposure event and an outcome.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/Outcome", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "population_context_qualifier": {"description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "temporal_context_qualifier": {"description": "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.", "format": "time", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToOutcomeAssociation", "type": "object"}, "ExposureEventToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToPhenotypicFeatureAssociation", "type": "object"}, "FDAApprovalStatusEnum": {"description": "", "enum": ["discovery_and_development_phase", "preclinical_research_phase", "fda_clinical_research_phase", "fda_review_phase_4", "fda_post_market_safety_review", "fda_clinical_research_phase_1", "fda_clinical_research_phase_2", "fda_clinical_research_phase_3", "fda_clinical_research_phase_4", "fda_fast_track", "fda_breakthrough_therapy", "fda_accelerated_approval", "fda_priority_review", "regular_fda_approval", "post_approval_withdrawal"], "title": "FDAApprovalStatusEnum", "type": "string"}, "FDAIDAAdverseEventEnum": {"description": "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32", "enum": ["life_threatening_adverse_event", "serious_adverse_event", "suspected_adverse_reaction", "unexpected_adverse_event"], "title": "FDAIDAAdverseEventEnum", "type": "string"}, "Food": {"additionalProperties": false, "description": "A substance consumed by a living organism as a source of nutrition", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Food", "type": "object"}, "FoodAdditive": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "FoodAdditive", "type": "object"}, "FunctionalAssociation": {"additionalProperties": false, "description": "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex that has the function associated with the GO term"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "FunctionalAssociation", "type": "object"}, "Gene": {"additionalProperties": false, "description": "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "symbol": {"description": "Symbol for a particular thing", "type": "string"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Gene", "type": "object"}, "GeneAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneAsAModelOfDiseaseAssociation", "type": "object"}, "GeneFamily": {"additionalProperties": false, "description": "any grouping of multiple genes or gene products related by common descent", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneFamily", "type": "object"}, "GeneHasVariantThatContributesToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "subject_form_or_variant_qualifier": {"type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneHasVariantThatContributesToDiseaseAssociation", "type": "object"}, "GeneOrGeneProductOrChemicalEntityAspectEnum": {"description": "", "enum": ["activity_or_abundance", "abundance", "activity", "expression", "synthesis", "degradation", "cleavage", "hydrolysis", "metabolic_processing", "mutation_rate", "stability", "folding", "localization", "transport", "secretion", "uptake", "molecular_modification", "acetylation", "acylation", "alkylation", "amination", "carbamoylation", "ethylation", "glutathionylation", "glycation", "glycosylation", "glucuronidation", "n_linked_glycosylation", "o_linked_glycosylation", "hydroxylation", "lipidation", "farnesylation", "geranoylation", "myristoylation", "palmitoylation", "prenylation", "methylation", "nitrosation", "nucleotidylation", "phosphorylation", "ribosylation", "ADP-ribosylation", "sulfation", "sumoylation", "ubiquitination", "oxidation", "reduction", "carboxylation"], "title": "GeneOrGeneProductOrChemicalEntityAspectEnum", "type": "string"}, "GeneOrGeneProductOrChemicalPartQualifierEnum": {"description": "", "enum": ["3_prime_utr", "5_prime_utr", "polya_tail", "promoter", "enhancer", "exon", "intron"], "title": "GeneOrGeneProductOrChemicalPartQualifierEnum", "type": "string"}, "GeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToDiseaseAssociation", "type": "object"}, "GeneToExpressionSiteAssociation": {"additionalProperties": false, "description": "An association between a gene and a gene expression site, possibly qualified by stage/timing info.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "location in which the gene is expressed", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "expression relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "can be used to indicate magnitude, or also ranking", "type": "string"}, "stage_qualifier": {"description": "stage at which the gene is expressed in the site", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToExpressionSiteAssociation", "type": "object"}, "GeneToGeneCoexpressionAssociation": {"additionalProperties": false, "description": "Indicates that two genes are co-expressed, generally under the same conditions.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneCoexpressionAssociation", "type": "object"}, "GeneToGeneFamilyAssociation": {"additionalProperties": false, "description": "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "membership of the gene in the given gene family.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneFamilyAssociation", "type": "object"}, "GeneToGeneHomologyAssociation": {"additionalProperties": false, "description": "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "homology relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneHomologyAssociation", "type": "object"}, "GeneToGeneProductRelationship": {"additionalProperties": false, "description": "A gene is transcribed and potentially translated to a gene product", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneProductMixin", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneProductRelationship", "type": "object"}, "GeneToGoTermAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "gene, product or macromolecular complex that has the function associated with the GO term", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGoTermAssociation", "type": "object"}, "GeneToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a gene or gene product and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that includes or is affected by the gene or gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product entity that participates or influences the pathway"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPathwayAssociation", "type": "object"}, "GeneToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the phenotypic feature"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPhenotypicFeatureAssociation", "type": "object"}, "GeneticInheritance": {"additionalProperties": false, "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneticInheritance", "type": "object"}, "Genome": {"additionalProperties": false, "description": "A genome is the sum of genetic material within a cell or virion.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genome", "type": "object"}, "GenomicBackgroundExposure": {"additionalProperties": false, "description": "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "has_attribute_type", "category"], "title": "GenomicBackgroundExposure", "type": "object"}, "GenomicSequenceLocalization": {"additionalProperties": false, "description": "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "end_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", "type": "integer"}, "genome_build": {"$ref": "#/$defs/StrandEnum", "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens."}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phase": {"$ref": "#/$defs/PhaseEnum", "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2."}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "start_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", "type": "integer"}, "strand": {"$ref": "#/$defs/StrandEnum", "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)."}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenomicSequenceLocalization", "type": "object"}, "Genotype": {"additionalProperties": false, "description": "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_zygosity": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genotype", "type": "object"}, "GenotypeAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A genotype that has a role in modeling the disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeAsAModelOfDiseaseAssociation", "type": "object"}, "GenotypeToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that genotype", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a genotype that is associated in some way with a disease state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToDiseaseAssociation", "type": "object"}, "GenotypeToGeneAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGeneAssociation", "type": "object"}, "GenotypeToGenotypePartAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a genotypic entity that is a sub-component of it", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "child genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGenotypePartAssociation", "type": "object"}, "GenotypeToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "genotype that is associated with the phenotypic feature", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToPhenotypicFeatureAssociation", "type": "object"}, "GenotypeToVariantAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a sequence variant.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToVariantAssociation", "type": "object"}, "GenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GenotypicSex", "type": "object"}, "GeographicExposure": {"additionalProperties": false, "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GeographicExposure", "type": "object"}, "GeographicLocation": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocation", "type": "object"}, "GeographicLocationAtTime": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates, for a particular time", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocationAtTime", "type": "object"}, "GrossAnatomicalStructure": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GrossAnatomicalStructure", "type": "object"}, "Haplotype": {"additionalProperties": false, "description": "A set of zero or more Alleles on a single instance of a Sequence[VMC]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Haplotype", "type": "object"}, "Hospitalization": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Hospitalization", "type": "object"}, "HospitalizationOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.", "title": "HospitalizationOutcome", "type": "object"}, "IndividualOrganism": {"additionalProperties": false, "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "IndividualOrganism", "type": "object"}, "InformationContentEntityToNamedThingAssociation": {"additionalProperties": false, "description": "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property).", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "InformationContentEntityToNamedThingAssociation", "type": "object"}, "InformationResource": {"additionalProperties": false, "description": "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "InformationResource", "type": "object"}, "LifeStage": {"additionalProperties": false, "description": "A stage of development or growth of an organism, including post-natal adult stages", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "LifeStage", "type": "object"}, "LogicalInterpretationEnum": {"description": "", "enum": ["some_some", "all_some", "inverse_all_some"], "title": "LogicalInterpretationEnum", "type": "string"}, "MacromolecularComplex": {"additionalProperties": false, "description": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MacromolecularComplex", "type": "object"}, "MacromolecularMachineToBiologicalProcessAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToBiologicalProcessAssociation", "type": "object"}, "MacromolecularMachineToCellularComponentAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToCellularComponentAssociation", "type": "object"}, "MacromolecularMachineToMolecularActivityAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToMolecularActivityAssociation", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MaterialSample", "type": "object"}, "MaterialSampleDerivationAssociation": {"additionalProperties": false, "description": "An association between a material sample and the material entity from which it is derived.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "derivation relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the material sample being described", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleDerivationAssociation", "type": "object"}, "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a material sample and a disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "MicroRNA": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MicroRNA", "type": "object"}, "MolecularActivity": {"additionalProperties": false, "description": "An execution of a molecular function carried out by a gene product or macromolecular complex.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "The gene product, gene, or complex that catalyzes the reaction", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "A chemical entity that is the input for the reaction", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "A chemical entity that is the output for the reaction", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularActivity", "type": "object"}, "MolecularActivityToChemicalEntityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToChemicalEntityAssociation", "type": "object"}, "MolecularActivityToMolecularActivityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToMolecularActivityAssociation", "type": "object"}, "MolecularActivityToPathwayAssociation": {"additionalProperties": false, "description": "Association that holds the relationship between a reaction and the pathway it participates in.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToPathwayAssociation", "type": "object"}, "MolecularEntity": {"additionalProperties": false, "description": "A molecular entity is a chemical entity composed of individual or covalently bonded atoms.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularEntity", "type": "object"}, "MolecularMixture": {"additionalProperties": false, "description": "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularMixture", "type": "object"}, "MortalityOutcome": {"additionalProperties": false, "description": "An outcome of death from resulting from an exposure event.", "title": "MortalityOutcome", "type": "object"}, "NamedThing": {"additionalProperties": false, "description": "a databased entity or concept/class", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NamedThing", "type": "object"}, "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation", "type": "object"}, "NoncodingRNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NoncodingRNAProduct", "type": "object"}, "NucleicAcidEntity": {"additionalProperties": false, "description": "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidEntity", "type": "object"}, "NucleicAcidSequenceMotif": {"additionalProperties": false, "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidSequenceMotif", "type": "object"}, "NucleosomeModification": {"additionalProperties": false, "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleosomeModification", "type": "object"}, "ObservedExpectedFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a observed expected frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ObservedExpectedFrequencyAnalysisResult", "type": "object"}, "Onset": {"additionalProperties": false, "description": "The age group in which (disease) symptom manifestations appear", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Onset", "type": "object"}, "OrganismAttribute": {"additionalProperties": false, "description": "describes a characteristic of an organismal entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "OrganismAttribute", "type": "object"}, "OrganismTaxon": {"additionalProperties": false, "description": "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "OrganismTaxon", "type": "object"}, "OrganismTaxonToOrganismTaxonInteraction": {"additionalProperties": false, "description": "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "associated_environmental_context": {"description": "the environment in which the two taxa interact", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the taxon that is the subject of the association", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the taxon that is the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonInteraction", "type": "object"}, "OrganismTaxonToOrganismTaxonSpecialization": {"additionalProperties": false, "description": "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the more general taxon", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the more specific taxon", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonSpecialization", "type": "object"}, "OrganismToOrganismAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between two individual organisms.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismToOrganismAssociation", "type": "object"}, "OrganismalEntityAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismalEntityAsAModelOfDiseaseAssociation", "type": "object"}, "PairwiseGeneToGeneInteraction": {"additionalProperties": false, "description": "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseGeneToGeneInteraction", "type": "object"}, "PairwiseMolecularInteraction": {"additionalProperties": false, "description": "An interaction at the molecular level between two physical entities", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "identifier for the interaction. This may come from an interaction database such as IMEX.", "type": "string"}, "interacting_molecules_category": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseMolecularInteraction", "type": "object"}, "PathologicalAnatomicalExposure": {"additionalProperties": false, "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalAnatomicalExposure", "type": "object"}, "PathologicalAnatomicalOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.", "title": "PathologicalAnatomicalOutcome", "type": "object"}, "PathologicalAnatomicalStructure": {"additionalProperties": false, "description": "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalAnatomicalStructure", "type": "object"}, "PathologicalProcess": {"additionalProperties": false, "description": "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalProcess", "type": "object"}, "PathologicalProcessExposure": {"additionalProperties": false, "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalProcessExposure", "type": "object"}, "PathologicalProcessOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of a pathological process.", "title": "PathologicalProcessOutcome", "type": "object"}, "Pathway": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Pathway", "type": "object"}, "PhaseEnum": {"description": "phase", "enum": ["0", "1", "2"], "title": "PhaseEnum", "type": "string"}, "Phenomenon": {"additionalProperties": false, "description": "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Phenomenon", "type": "object"}, "PhenotypicFeature": {"additionalProperties": false, "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhenotypicFeature", "type": "object"}, "PhenotypicQuality": {"additionalProperties": false, "description": "A property of a phenotype", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicQuality", "type": "object"}, "PhenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicSex", "type": "object"}, "PhysicalEntity": {"additionalProperties": false, "description": "An entity that has material reality (a.k.a. physical essence).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysicalEntity", "type": "object"}, "PhysiologicalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysiologicalProcess", "type": "object"}, "PlanetaryEntity": {"additionalProperties": false, "description": "Any entity or process that exists at the level of the whole planet", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PlanetaryEntity", "type": "object"}, "Polypeptide": {"additionalProperties": false, "description": "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Polypeptide", "type": "object"}, "PopulationOfIndividualOrganisms": {"additionalProperties": false, "description": "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PopulationOfIndividualOrganisms", "type": "object"}, "PopulationToPopulationAssociation": {"additionalProperties": false, "description": "An association between a two populations", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that form the object of the association", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the population that form the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "PopulationToPopulationAssociation", "type": "object"}, "PosttranslationalModification": {"additionalProperties": false, "description": "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PosttranslationalModification", "type": "object"}, "PredicateMapping": {"additionalProperties": false, "description": "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.", "properties": {"anatomical_context_qualifier": {"$ref": "#/$defs/AnatomicalContextQualifierEnum", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)."}, "broad_match": {"description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"$ref": "#/$defs/CausalMechanismQualifierEnum", "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')"}, "exact_match": {"description": "holds between two entities that have strictly equivalent meanings, with a high degree of confidence", "items": {"type": "string"}, "type": "array"}, "mapped_predicate": {"description": "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.", "type": "string"}, "narrow_match": {"description": "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "object_aspect_qualifier": {"type": "string"}, "object_context_qualifier": {"type": "string"}, "object_derivative_qualifier": {"type": "string"}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "object_form_or_variant_qualifier": {"type": "string"}, "object_part_qualifier": {"type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "species_context_qualifier": {"description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", "type": "string"}, "subject_aspect_qualifier": {"type": "string"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"type": "string"}, "subject_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "subject_form_or_variant_qualifier": {"type": "string"}, "subject_part_qualifier": {"type": "string"}}, "required": ["predicate"], "title": "PredicateMapping", "type": "object"}, "Procedure": {"additionalProperties": false, "description": "A series of actions conducted in a certain order or manner", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Procedure", "type": "object"}, "ProcessedMaterial": {"additionalProperties": false, "description": "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProcessedMaterial", "type": "object"}, "Protein": {"additionalProperties": false, "description": "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Protein", "type": "object"}, "ProteinDomain": {"additionalProperties": false, "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinDomain", "type": "object"}, "ProteinFamily": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinFamily", "type": "object"}, "ProteinIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinIsoform", "type": "object"}, "Publication": {"additionalProperties": false, "description": "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", "type": "string"}, "pages": {"description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Publication", "type": "object"}, "QuantityValue": {"additionalProperties": false, "description": "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value", "properties": {"has_numeric_value": {"description": "connects a quantity value to a number", "type": "number"}, "has_unit": {"description": "connects a quantity value to a unit", "type": "string"}}, "title": "QuantityValue", "type": "object"}, "RNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProduct", "type": "object"}, "RNAProductIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference RNA", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProductIsoform", "type": "object"}, "ReactionDirectionEnum": {"description": "", "enum": ["left_to_right", "right_to_left", "bidirectional", "neutral"], "title": "ReactionDirectionEnum", "type": "string"}, "ReactionSideEnum": {"description": "", "enum": ["left", "right"], "title": "ReactionSideEnum", "type": "string"}, "ReactionToCatalystAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToCatalystAssociation", "type": "object"}, "ReactionToParticipantAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToParticipantAssociation", "type": "object"}, "ReagentTargetedGene": {"additionalProperties": false, "description": "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ReagentTargetedGene", "type": "object"}, "RegulatoryRegion": {"additionalProperties": false, "description": "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RegulatoryRegion", "type": "object"}, "RelationshipType": {"additionalProperties": false, "description": "An OWL property used as an edge label", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "RelationshipType", "type": "object"}, "RelativeFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a relative frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RelativeFrequencyAnalysisResult", "type": "object"}, "ResourceRoleEnum": {"description": "The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience.", "enum": ["primary_knowledge_source", "aggregator_knowledge_source", "supporting_data_source"], "title": "ResourceRoleEnum", "type": "string"}, "RetrievalSource": {"additionalProperties": false, "description": "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "resource": {"description": "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", "type": "string"}, "resource_role": {"$ref": "#/$defs/ResourceRoleEnum", "description": "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge."}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "upstream_resources": {"description": "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["resource", "resource_role", "id", "category"], "title": "RetrievalSource", "type": "object"}, "SequenceAssociation": {"additionalProperties": false, "description": "An association between a sequence feature and a nucleic acid entity it is localized to.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceAssociation", "type": "object"}, "SequenceEnum": {"description": "type of sequence", "enum": ["na", "aa"], "title": "SequenceEnum", "type": "string"}, "SequenceFeatureRelationship": {"additionalProperties": false, "description": "For example, a particular exon is part of a particular transcript or gene", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceFeatureRelationship", "type": "object"}, "SequenceVariant": {"additionalProperties": false, "description": "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "The state of the sequence w.r.t a reference sequence", "type": "string"}, "has_gene": {"description": "Each allele can be associated with any number of genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SequenceVariant", "type": "object"}, "Serial": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Serials (journals) should have industry-standard identifier such as from ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "items": {"type": "string"}, "type": "array"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Serial", "type": "object"}, "SeverityValue": {"additionalProperties": false, "description": "describes the severity of a phenotypic feature or disease", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SeverityValue", "type": "object"}, "SiRNA": {"additionalProperties": false, "description": "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SiRNA", "type": "object"}, "SmallMolecule": {"additionalProperties": false, "description": "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SmallMolecule", "type": "object"}, "Snv": {"additionalProperties": false, "description": "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene": {"description": "connects an entity associated with one or more genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Snv", "type": "object"}, "SocioeconomicAttribute": {"additionalProperties": false, "description": "Attributes relating to a socioeconomic manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SocioeconomicAttribute", "type": "object"}, "SocioeconomicExposure": {"additionalProperties": false, "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category", "has_attribute"], "title": "SocioeconomicExposure", "type": "object"}, "SocioeconomicOutcome": {"additionalProperties": false, "description": "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event", "title": "SocioeconomicOutcome", "type": "object"}, "StrandEnum": {"description": "strand", "enum": ["+", "-", ".", "?"], "title": "StrandEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "a detailed investigation and/or analysis", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Study", "type": "object"}, "StudyPopulation": {"additionalProperties": false, "description": "A group of people banded together or treated as a group as participants in a research study.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyPopulation", "type": "object"}, "StudyVariable": {"additionalProperties": false, "description": "a variable that is used as a measure in the investigation of a study", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyVariable", "type": "object"}, "TaxonToTaxonAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between individuals of different taxa.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "TaxonToTaxonAssociation", "type": "object"}, "TaxonomicRank": {"additionalProperties": false, "description": "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "TaxonomicRank", "type": "object"}, "TextMiningResult": {"additionalProperties": false, "description": "A result of text mining.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "TextMiningResult", "type": "object"}, "Transcript": {"additionalProperties": false, "description": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Transcript", "type": "object"}, "TranscriptToGeneRelationship": {"additionalProperties": false, "description": "A gene is a collection of transcripts", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "TranscriptToGeneRelationship", "type": "object"}, "TranscriptionFactorBindingSite": {"additionalProperties": false, "description": "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "TranscriptionFactorBindingSite", "type": "object"}, "Treatment": {"additionalProperties": false, "description": "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_device": {"description": "connects an entity to one or more (medical) devices", "items": {"type": "string"}, "type": "array"}, "has_drug": {"description": "connects an entity to one or more drugs", "items": {"type": "string"}, "type": "array"}, "has_procedure": {"description": "connects an entity to one or more (medical) procedures", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Treatment", "type": "object"}, "VariantAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A variant that has a role in modeling the disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantAsAModelOfDiseaseAssociation", "type": "object"}, "VariantToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that variant", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the disease state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToDiseaseAssociation", "type": "object"}, "VariantToGeneAssociation": {"additionalProperties": false, "description": "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneAssociation", "type": "object"}, "VariantToGeneExpressionAssociation": {"additionalProperties": false, "description": "An association between a variant and expression of a gene (i.e. e-QTL)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneExpressionAssociation", "type": "object"}, "VariantToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the phenotype state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPhenotypicFeatureAssociation", "type": "object"}, "VariantToPopulationAssociation": {"additionalProperties": false, "description": "An association between a variant and a population, where the variant has particular frequency in the population", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number in object population that carry a particular allele, aka allele count", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", "type": "number"}, "has_total": {"description": "number all populations that carry a particular allele, aka allele number", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that is observed to have the frequency", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "an allele that has a certain frequency in a given population", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPopulationAssociation", "type": "object"}, "Virus": {"additionalProperties": false, "description": "A virus is a microorganism that replicates itself as a microRNA and infects the host cell.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Virus", "type": "object"}, "Zygosity": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Zygosity", "type": "object"}}, "$id": "https://w3id.org/biolink/biolink-model", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": true, "metamodel_version": "1.7.0", "title": "Biolink-Model", "type": "object", "version": "3.2.5"} +{"$defs": {"AccessibleDnaRegion": {"additionalProperties": false, "description": "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "AccessibleDnaRegion", "type": "object"}, "Activity": {"additionalProperties": false, "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "person, group, organization or project that provides a piece of information (i.e. a knowledge association)", "properties": {"address": {"description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", "type": "string"}, "affiliation": {"description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Agent", "type": "object"}, "AnatomicalContextQualifierEnum": {"description": "", "enum": [], "title": "AnatomicalContextQualifierEnum", "type": "string"}, "AnatomicalEntity": {"additionalProperties": false, "description": "A subcellular location, cell type or gross anatomical part", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "AnatomicalEntity", "type": "object"}, "AnatomicalEntityToAnatomicalEntityOntogenicAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the structure at an earlier time", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the structure at a later time", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityOntogenicAssociation", "type": "object"}, "AnatomicalEntityToAnatomicalEntityPartOfAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the whole", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the part", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityPartOfAssociation", "type": "object"}, "Article": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent serial containing the article should have industry-standard identifier from ISSN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category"], "title": "Article", "type": "object"}, "Association": {"additionalProperties": false, "description": "A typed association between two entities, supported by evidence", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "Association", "type": "object"}, "Attribute": {"additionalProperties": false, "description": "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Attribute", "type": "object"}, "Behavior": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Behavior", "type": "object"}, "BehaviorToBehavioralFeatureAssociation": {"additionalProperties": false, "description": "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "behavioral feature that is the object of the association", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "behavior that is the subject of the association", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "BehaviorToBehavioralFeatureAssociation", "type": "object"}, "BehavioralExposure": {"additionalProperties": false, "description": "A behavioral exposure is a factor relating to behavior impacting an individual.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BehavioralExposure", "type": "object"}, "BehavioralFeature": {"additionalProperties": false, "description": "A phenotypic feature which is behavioral in nature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BehavioralFeature", "type": "object"}, "BehavioralOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of human behavior.", "title": "BehavioralOutcome", "type": "object"}, "BiologicalProcess": {"additionalProperties": false, "description": "One or more causally connected executions of molecular functions", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcess", "type": "object"}, "BiologicalProcessOrActivity": {"additionalProperties": false, "description": "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcessOrActivity", "type": "object"}, "BiologicalSex": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BiologicalSex", "type": "object"}, "BioticExposure": {"additionalProperties": false, "description": "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BioticExposure", "type": "object"}, "Book": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Books should have industry-standard identifier such as from ISBN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'book'.", "items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Book", "type": "object"}, "BookChapter": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "chapter": {"description": "chapter of a book", "type": "string"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category"], "title": "BookChapter", "type": "object"}, "Case": {"additionalProperties": false, "description": "An individual (human) organism that has a patient role in some clinical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Case", "type": "object"}, "CaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "CaseToPhenotypicFeatureAssociation", "type": "object"}, "CausalMechanismQualifierEnum": {"description": "", "enum": ["binding", "inhibition", "antibody_inhibition", "antagonism", "molecular_channel_blockage", "inverse_agonism", "negative_allosteric_modulation", "agonism", "molecular_channel_opening", "positive_allosteric_modulation", "potentiation", "activation", "inducer", "transcriptional_regulation", "signaling_mediated_control", "stabilization", "stimulation", "releasing_activity"], "title": "CausalMechanismQualifierEnum", "type": "string"}, "Cell": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cell", "type": "object"}, "CellLine": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellLine", "type": "object"}, "CellLineAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineAsAModelOfDiseaseAssociation", "type": "object"}, "CellLineToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "CellularComponent": {"additionalProperties": false, "description": "A location in or around a cell", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularComponent", "type": "object"}, "CellularOrganism": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularOrganism", "type": "object"}, "ChemicalAffectsGeneAssociation": {"additionalProperties": false, "description": "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"$ref": "#/$defs/CausalMechanismQualifierEnum", "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalAffectsGeneAssociation", "type": "object"}, "ChemicalEntity": {"additionalProperties": false, "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalEntity", "type": "object"}, "ChemicalEntityAssessesNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityAssessesNamedThingAssociation", "type": "object"}, "ChemicalEntityDerivativeEnum": {"description": "", "enum": ["metabolite"], "title": "ChemicalEntityDerivativeEnum", "type": "string"}, "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation": {"additionalProperties": false, "description": "A regulatory relationship between two genes", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the direction is always from regulator to regulated", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation", "type": "object"}, "ChemicalExposure": {"additionalProperties": false, "description": "A chemical exposure is an intake of a particular chemical entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalExposure", "type": "object"}, "ChemicalGeneInteractionAssociation": {"additionalProperties": false, "description": "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalGeneInteractionAssociation", "type": "object"}, "ChemicalMixture": {"additionalProperties": false, "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalMixture", "type": "object"}, "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrGeneOrGeneProductFormOrVariantEnum": {"description": "", "enum": ["genetic_variant_form", "modified_form", "loss_of_function_variant_form", "gain_of_function_variant_form", "polymorphic_form", "snp_form", "analog_form"], "title": "ChemicalOrGeneOrGeneProductFormOrVariantEnum", "type": "string"}, "ChemicalRole": {"additionalProperties": false, "description": "A role played by the molecular entity or part thereof within a chemical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalRole", "type": "object"}, "ChemicalToChemicalAssociation": {"additionalProperties": false, "description": "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the chemical element that is the target of the statement", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalAssociation", "type": "object"}, "ChemicalToChemicalDerivationAssociation": {"additionalProperties": false, "description": "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "catalyst_qualifier": {"description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the downstream chemical entity", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the upstream chemical entity", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalDerivationAssociation", "type": "object"}, "ChemicalToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the disease or phenotype that is affected by the chemical", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that is affected by the chemical", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the chemical entity that is affecting the pathway", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToPathwayAssociation", "type": "object"}, "ChiSquaredAnalysisResult": {"additionalProperties": false, "description": "A result of a chi squared analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChiSquaredAnalysisResult", "type": "object"}, "ClinicalAttribute": {"additionalProperties": false, "description": "Attributes relating to a clinical manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalAttribute", "type": "object"}, "ClinicalCourse": {"additionalProperties": false, "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalCourse", "type": "object"}, "ClinicalEntity": {"additionalProperties": false, "description": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalEntity", "type": "object"}, "ClinicalFinding": {"additionalProperties": false, "description": "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalFinding", "type": "object"}, "ClinicalIntervention": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalIntervention", "type": "object"}, "ClinicalMeasurement": {"additionalProperties": false, "description": "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalMeasurement", "type": "object"}, "ClinicalModifier": {"additionalProperties": false, "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalModifier", "type": "object"}, "ClinicalTrial": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalTrial", "type": "object"}, "CodingSequence": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CodingSequence", "type": "object"}, "Cohort": {"additionalProperties": false, "description": "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cohort", "type": "object"}, "CommonDataElement": {"additionalProperties": false, "description": "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CommonDataElement", "type": "object"}, "ComplexChemicalExposure": {"additionalProperties": false, "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ComplexChemicalExposure", "type": "object"}, "ComplexMolecularMixture": {"additionalProperties": false, "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ComplexMolecularMixture", "type": "object"}, "ConceptCountAnalysisResult": {"additionalProperties": false, "description": "A result of a concept count analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConceptCountAnalysisResult", "type": "object"}, "ConfidenceLevel": {"additionalProperties": false, "description": "Level of confidence in a statement", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConfidenceLevel", "type": "object"}, "ContributorAssociation": {"additionalProperties": false, "description": "Any association between an entity (such as a publication) and various agents that contribute to its realisation", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "agent helping to realise the given entity (e.g. such as a publication)", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "information content entity which an agent has helped realise", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ContributorAssociation", "type": "object"}, "Dataset": {"additionalProperties": false, "description": "an item that refers to a collection of data from a data source.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Dataset", "type": "object"}, "DatasetDistribution": {"additionalProperties": false, "description": "an item that holds distribution level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "distribution_download_url": {"type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetDistribution", "type": "object"}, "DatasetSummary": {"additionalProperties": false, "description": "an item that holds summary level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "source_logo": {"type": "string"}, "source_web_page": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetSummary", "type": "object"}, "DatasetVersion": {"additionalProperties": false, "description": "an item that holds version level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_dataset": {"type": "string"}, "has_distribution": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "ingest_date": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetVersion", "type": "object"}, "Device": {"additionalProperties": false, "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Device", "type": "object"}, "DirectionQualifierEnum": {"description": "", "enum": ["increased", "upregulated", "decreased", "downregulated"], "title": "DirectionQualifierEnum", "type": "string"}, "Disease": {"additionalProperties": false, "description": "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Disease", "type": "object"}, "DiseaseOrPhenotypicFeature": {"additionalProperties": false, "description": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DiseaseOrPhenotypicFeature", "type": "object"}, "DiseaseOrPhenotypicFeatureExposure": {"additionalProperties": false, "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DiseaseOrPhenotypicFeatureExposure", "type": "object"}, "DiseaseOrPhenotypicFeatureOutcome": {"additionalProperties": false, "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.", "title": "DiseaseOrPhenotypicFeatureOutcome", "type": "object"}, "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "genetic inheritance associated with the specified disease or phenotypic feature.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "type": "object"}, "DiseaseOrPhenotypicFeatureToLocationAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "anatomical entity in which the disease or feature is found.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToLocationAssociation", "type": "object"}, "DiseaseToExposureEventAssociation": {"additionalProperties": false, "description": "An association between an exposure event and a disease.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToExposureEventAssociation", "type": "object"}, "DiseaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToPhenotypicFeatureAssociation", "type": "object"}, "Drug": {"additionalProperties": false, "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Drug", "type": "object"}, "DrugAvailabilityEnum": {"description": "", "enum": ["over_the_counter", "prescription"], "title": "DrugAvailabilityEnum", "type": "string"}, "DrugDeliveryEnum": {"description": "", "enum": ["inhalation", "oral", "absorption_through_the_skin", "intravenous_injection"], "title": "DrugDeliveryEnum", "type": "string"}, "DrugExposure": {"additionalProperties": false, "description": "A drug exposure is an intake of a particular drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugExposure", "type": "object"}, "DrugToGeneAssociation": {"additionalProperties": false, "description": "An interaction between a drug and a gene or gene product.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product that is affected by the drug"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DrugToGeneAssociation", "type": "object"}, "DrugToGeneInteractionExposure": {"additionalProperties": false, "description": "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugToGeneInteractionExposure", "type": "object"}, "DruggableGeneCategoryEnum": {"description": "", "enum": ["tclin", "tbio", "tchem", "tdark"], "title": "DruggableGeneCategoryEnum", "type": "string"}, "DruggableGeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"$ref": "#/$defs/DruggableGeneCategoryEnum"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "DruggableGeneToDiseaseAssociation", "type": "object"}, "EntityToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToDiseaseAssociation", "type": "object"}, "EntityToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToPhenotypicFeatureAssociation", "type": "object"}, "EnvironmentalExposure": {"additionalProperties": false, "description": "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "EnvironmentalExposure", "type": "object"}, "EnvironmentalFeature": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFeature", "type": "object"}, "EnvironmentalFoodContaminant": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFoodContaminant", "type": "object"}, "EnvironmentalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalProcess", "type": "object"}, "EpidemiologicalOutcome": {"additionalProperties": false, "description": "An epidemiological outcome, such as societal disease burden, resulting from an exposure event.", "title": "EpidemiologicalOutcome", "type": "object"}, "Event": {"additionalProperties": false, "description": "Something that happens at a given place and time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Event", "type": "object"}, "EvidenceType": {"additionalProperties": false, "description": "Class of evidence that supports an association", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EvidenceType", "type": "object"}, "Exon": {"additionalProperties": false, "description": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Exon", "type": "object"}, "ExonToTranscriptRelationship": {"additionalProperties": false, "description": "A transcript is formed from multiple exons", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExonToTranscriptRelationship", "type": "object"}, "ExposureEventToOutcomeAssociation": {"additionalProperties": false, "description": "An association between an exposure event and an outcome.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/Outcome", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "population_context_qualifier": {"description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "temporal_context_qualifier": {"description": "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.", "format": "time", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToOutcomeAssociation", "type": "object"}, "ExposureEventToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToPhenotypicFeatureAssociation", "type": "object"}, "FDAApprovalStatusEnum": {"description": "", "enum": ["discovery_and_development_phase", "preclinical_research_phase", "fda_clinical_research_phase", "fda_review_phase_4", "fda_post_market_safety_review", "fda_clinical_research_phase_1", "fda_clinical_research_phase_2", "fda_clinical_research_phase_3", "fda_clinical_research_phase_4", "fda_fast_track", "fda_breakthrough_therapy", "fda_accelerated_approval", "fda_priority_review", "regular_fda_approval", "post_approval_withdrawal"], "title": "FDAApprovalStatusEnum", "type": "string"}, "FDAIDAAdverseEventEnum": {"description": "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32", "enum": ["life_threatening_adverse_event", "serious_adverse_event", "suspected_adverse_reaction", "unexpected_adverse_event"], "title": "FDAIDAAdverseEventEnum", "type": "string"}, "Food": {"additionalProperties": false, "description": "A substance consumed by a living organism as a source of nutrition", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Food", "type": "object"}, "FoodAdditive": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "FoodAdditive", "type": "object"}, "FunctionalAssociation": {"additionalProperties": false, "description": "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex that has the function associated with the GO term"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "FunctionalAssociation", "type": "object"}, "Gene": {"additionalProperties": false, "description": "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "symbol": {"description": "Symbol for a particular thing", "type": "string"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Gene", "type": "object"}, "GeneAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneAsAModelOfDiseaseAssociation", "type": "object"}, "GeneFamily": {"additionalProperties": false, "description": "any grouping of multiple genes or gene products related by common descent", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneFamily", "type": "object"}, "GeneHasVariantThatContributesToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_form_or_variant_qualifier": {"type": "string"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneHasVariantThatContributesToDiseaseAssociation", "type": "object"}, "GeneOrGeneProductOrChemicalEntityAspectEnum": {"description": "", "enum": ["activity_or_abundance", "abundance", "activity", "expression", "synthesis", "degradation", "cleavage", "hydrolysis", "metabolic_processing", "mutation_rate", "stability", "folding", "localization", "transport", "secretion", "uptake", "molecular_modification", "acetylation", "acylation", "alkylation", "amination", "carbamoylation", "ethylation", "glutathionylation", "glycation", "glycosylation", "glucuronidation", "n_linked_glycosylation", "o_linked_glycosylation", "hydroxylation", "lipidation", "farnesylation", "geranoylation", "myristoylation", "palmitoylation", "prenylation", "methylation", "nitrosation", "nucleotidylation", "phosphorylation", "ribosylation", "ADP-ribosylation", "sulfation", "sumoylation", "ubiquitination", "oxidation", "reduction", "carboxylation"], "title": "GeneOrGeneProductOrChemicalEntityAspectEnum", "type": "string"}, "GeneOrGeneProductOrChemicalPartQualifierEnum": {"description": "", "enum": ["3_prime_utr", "5_prime_utr", "polya_tail", "promoter", "enhancer", "exon", "intron"], "title": "GeneOrGeneProductOrChemicalPartQualifierEnum", "type": "string"}, "GeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToDiseaseAssociation", "type": "object"}, "GeneToExpressionSiteAssociation": {"additionalProperties": false, "description": "An association between a gene and a gene expression site, possibly qualified by stage/timing info.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "location in which the gene is expressed", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "expression relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "can be used to indicate magnitude, or also ranking", "type": "string"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "stage_qualifier": {"description": "stage at which the gene is expressed in the site", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToExpressionSiteAssociation", "type": "object"}, "GeneToGeneCoexpressionAssociation": {"additionalProperties": false, "description": "Indicates that two genes are co-expressed, generally under the same conditions.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneCoexpressionAssociation", "type": "object"}, "GeneToGeneFamilyAssociation": {"additionalProperties": false, "description": "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "membership of the gene in the given gene family.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneFamilyAssociation", "type": "object"}, "GeneToGeneHomologyAssociation": {"additionalProperties": false, "description": "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "homology relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneHomologyAssociation", "type": "object"}, "GeneToGeneProductRelationship": {"additionalProperties": false, "description": "A gene is transcribed and potentially translated to a gene product", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneProductMixin", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneProductRelationship", "type": "object"}, "GeneToGoTermAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "gene, product or macromolecular complex that has the function associated with the GO term", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGoTermAssociation", "type": "object"}, "GeneToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a gene or gene product and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that includes or is affected by the gene or gene product", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product entity that participates or influences the pathway"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPathwayAssociation", "type": "object"}, "GeneToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the phenotypic feature"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPhenotypicFeatureAssociation", "type": "object"}, "GeneticInheritance": {"additionalProperties": false, "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneticInheritance", "type": "object"}, "Genome": {"additionalProperties": false, "description": "A genome is the sum of genetic material within a cell or virion.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genome", "type": "object"}, "GenomicBackgroundExposure": {"additionalProperties": false, "description": "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "has_attribute_type", "category"], "title": "GenomicBackgroundExposure", "type": "object"}, "GenomicSequenceLocalization": {"additionalProperties": false, "description": "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "end_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", "type": "integer"}, "genome_build": {"$ref": "#/$defs/StrandEnum", "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens."}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phase": {"$ref": "#/$defs/PhaseEnum", "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2."}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "start_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", "type": "integer"}, "strand": {"$ref": "#/$defs/StrandEnum", "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)."}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenomicSequenceLocalization", "type": "object"}, "Genotype": {"additionalProperties": false, "description": "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_zygosity": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genotype", "type": "object"}, "GenotypeAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A genotype that has a role in modeling the disease.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeAsAModelOfDiseaseAssociation", "type": "object"}, "GenotypeToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that genotype", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a genotype that is associated in some way with a disease state", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToDiseaseAssociation", "type": "object"}, "GenotypeToGeneAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGeneAssociation", "type": "object"}, "GenotypeToGenotypePartAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a genotypic entity that is a sub-component of it", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "child genotype", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGenotypePartAssociation", "type": "object"}, "GenotypeToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "genotype that is associated with the phenotypic feature", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToPhenotypicFeatureAssociation", "type": "object"}, "GenotypeToVariantAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a sequence variant.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToVariantAssociation", "type": "object"}, "GenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GenotypicSex", "type": "object"}, "GeographicExposure": {"additionalProperties": false, "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GeographicExposure", "type": "object"}, "GeographicLocation": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocation", "type": "object"}, "GeographicLocationAtTime": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates, for a particular time", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocationAtTime", "type": "object"}, "GrossAnatomicalStructure": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GrossAnatomicalStructure", "type": "object"}, "Haplotype": {"additionalProperties": false, "description": "A set of zero or more Alleles on a single instance of a Sequence[VMC]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Haplotype", "type": "object"}, "Hospitalization": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Hospitalization", "type": "object"}, "HospitalizationOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.", "title": "HospitalizationOutcome", "type": "object"}, "IndividualOrganism": {"additionalProperties": false, "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "IndividualOrganism", "type": "object"}, "InformationContentEntityToNamedThingAssociation": {"additionalProperties": false, "description": "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property).", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "InformationContentEntityToNamedThingAssociation", "type": "object"}, "InformationResource": {"additionalProperties": false, "description": "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "InformationResource", "type": "object"}, "LifeStage": {"additionalProperties": false, "description": "A stage of development or growth of an organism, including post-natal adult stages", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "LifeStage", "type": "object"}, "LogicalInterpretationEnum": {"description": "", "enum": ["some_some", "all_some", "inverse_all_some"], "title": "LogicalInterpretationEnum", "type": "string"}, "MacromolecularComplex": {"additionalProperties": false, "description": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MacromolecularComplex", "type": "object"}, "MacromolecularMachineToBiologicalProcessAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToBiologicalProcessAssociation", "type": "object"}, "MacromolecularMachineToCellularComponentAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToCellularComponentAssociation", "type": "object"}, "MacromolecularMachineToMolecularActivityAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToMolecularActivityAssociation", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MaterialSample", "type": "object"}, "MaterialSampleDerivationAssociation": {"additionalProperties": false, "description": "An association between a material sample and the material entity from which it is derived.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "derivation relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the material sample being described", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleDerivationAssociation", "type": "object"}, "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a material sample and a disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "MicroRNA": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MicroRNA", "type": "object"}, "MolecularActivity": {"additionalProperties": false, "description": "An execution of a molecular function carried out by a gene product or macromolecular complex.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "The gene product, gene, or complex that catalyzes the reaction", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "A chemical entity that is the input for the reaction", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "A chemical entity that is the output for the reaction", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularActivity", "type": "object"}, "MolecularActivityToChemicalEntityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToChemicalEntityAssociation", "type": "object"}, "MolecularActivityToMolecularActivityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToMolecularActivityAssociation", "type": "object"}, "MolecularActivityToPathwayAssociation": {"additionalProperties": false, "description": "Association that holds the relationship between a reaction and the pathway it participates in.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToPathwayAssociation", "type": "object"}, "MolecularEntity": {"additionalProperties": false, "description": "A molecular entity is a chemical entity composed of individual or covalently bonded atoms.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularEntity", "type": "object"}, "MolecularMixture": {"additionalProperties": false, "description": "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularMixture", "type": "object"}, "MortalityOutcome": {"additionalProperties": false, "description": "An outcome of death from resulting from an exposure event.", "title": "MortalityOutcome", "type": "object"}, "NamedThing": {"additionalProperties": false, "description": "a databased entity or concept/class", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NamedThing", "type": "object"}, "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation", "type": "object"}, "NoncodingRNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NoncodingRNAProduct", "type": "object"}, "NucleicAcidEntity": {"additionalProperties": false, "description": "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidEntity", "type": "object"}, "NucleicAcidSequenceMotif": {"additionalProperties": false, "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidSequenceMotif", "type": "object"}, "NucleosomeModification": {"additionalProperties": false, "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleosomeModification", "type": "object"}, "ObservedExpectedFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a observed expected frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ObservedExpectedFrequencyAnalysisResult", "type": "object"}, "Onset": {"additionalProperties": false, "description": "The age group in which (disease) symptom manifestations appear", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Onset", "type": "object"}, "OrganismAttribute": {"additionalProperties": false, "description": "describes a characteristic of an organismal entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "OrganismAttribute", "type": "object"}, "OrganismTaxon": {"additionalProperties": false, "description": "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "OrganismTaxon", "type": "object"}, "OrganismTaxonToOrganismTaxonInteraction": {"additionalProperties": false, "description": "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "associated_environmental_context": {"description": "the environment in which the two taxa interact", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the taxon that is the subject of the association", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the taxon that is the subject of the association", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonInteraction", "type": "object"}, "OrganismTaxonToOrganismTaxonSpecialization": {"additionalProperties": false, "description": "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the more general taxon", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the more specific taxon", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonSpecialization", "type": "object"}, "OrganismToOrganismAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between two individual organisms.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismToOrganismAssociation", "type": "object"}, "OrganismalEntityAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismalEntityAsAModelOfDiseaseAssociation", "type": "object"}, "PairwiseGeneToGeneInteraction": {"additionalProperties": false, "description": "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseGeneToGeneInteraction", "type": "object"}, "PairwiseMolecularInteraction": {"additionalProperties": false, "description": "An interaction at the molecular level between two physical entities", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "identifier for the interaction. This may come from an interaction database such as IMEX.", "type": "string"}, "interacting_molecules_category": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseMolecularInteraction", "type": "object"}, "PathologicalAnatomicalExposure": {"additionalProperties": false, "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalAnatomicalExposure", "type": "object"}, "PathologicalAnatomicalOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.", "title": "PathologicalAnatomicalOutcome", "type": "object"}, "PathologicalAnatomicalStructure": {"additionalProperties": false, "description": "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalAnatomicalStructure", "type": "object"}, "PathologicalProcess": {"additionalProperties": false, "description": "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalProcess", "type": "object"}, "PathologicalProcessExposure": {"additionalProperties": false, "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalProcessExposure", "type": "object"}, "PathologicalProcessOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of a pathological process.", "title": "PathologicalProcessOutcome", "type": "object"}, "Pathway": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Pathway", "type": "object"}, "PhaseEnum": {"description": "phase", "enum": ["0", "1", "2"], "title": "PhaseEnum", "type": "string"}, "Phenomenon": {"additionalProperties": false, "description": "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Phenomenon", "type": "object"}, "PhenotypicFeature": {"additionalProperties": false, "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhenotypicFeature", "type": "object"}, "PhenotypicQuality": {"additionalProperties": false, "description": "A property of a phenotype", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicQuality", "type": "object"}, "PhenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicSex", "type": "object"}, "PhysicalEntity": {"additionalProperties": false, "description": "An entity that has material reality (a.k.a. physical essence).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysicalEntity", "type": "object"}, "PhysiologicalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysiologicalProcess", "type": "object"}, "PlanetaryEntity": {"additionalProperties": false, "description": "Any entity or process that exists at the level of the whole planet", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PlanetaryEntity", "type": "object"}, "Polypeptide": {"additionalProperties": false, "description": "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Polypeptide", "type": "object"}, "PopulationOfIndividualOrganisms": {"additionalProperties": false, "description": "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PopulationOfIndividualOrganisms", "type": "object"}, "PopulationToPopulationAssociation": {"additionalProperties": false, "description": "An association between a two populations", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that form the object of the association", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the population that form the subject of the association", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "PopulationToPopulationAssociation", "type": "object"}, "PosttranslationalModification": {"additionalProperties": false, "description": "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PosttranslationalModification", "type": "object"}, "PredicateMapping": {"additionalProperties": false, "description": "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.", "properties": {"anatomical_context_qualifier": {"$ref": "#/$defs/AnatomicalContextQualifierEnum", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)."}, "broad_match": {"description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"$ref": "#/$defs/CausalMechanismQualifierEnum", "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')"}, "exact_match": {"description": "holds between two entities that have strictly equivalent meanings, with a high degree of confidence", "items": {"type": "string"}, "type": "array"}, "mapped_predicate": {"description": "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.", "type": "string"}, "narrow_match": {"description": "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "object_aspect_qualifier": {"type": "string"}, "object_context_qualifier": {"type": "string"}, "object_derivative_qualifier": {"type": "string"}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "object_form_or_variant_qualifier": {"type": "string"}, "object_part_qualifier": {"type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "species_context_qualifier": {"description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", "type": "string"}, "subject_aspect_qualifier": {"type": "string"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"type": "string"}, "subject_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "subject_form_or_variant_qualifier": {"type": "string"}, "subject_part_qualifier": {"type": "string"}}, "required": ["predicate"], "title": "PredicateMapping", "type": "object"}, "Procedure": {"additionalProperties": false, "description": "A series of actions conducted in a certain order or manner", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Procedure", "type": "object"}, "ProcessedMaterial": {"additionalProperties": false, "description": "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProcessedMaterial", "type": "object"}, "Protein": {"additionalProperties": false, "description": "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Protein", "type": "object"}, "ProteinDomain": {"additionalProperties": false, "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinDomain", "type": "object"}, "ProteinFamily": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinFamily", "type": "object"}, "ProteinIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinIsoform", "type": "object"}, "Publication": {"additionalProperties": false, "description": "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", "type": "string"}, "pages": {"description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Publication", "type": "object"}, "QuantityValue": {"additionalProperties": false, "description": "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value", "properties": {"has_numeric_value": {"description": "connects a quantity value to a number", "type": "number"}, "has_unit": {"description": "connects a quantity value to a unit", "type": "string"}}, "title": "QuantityValue", "type": "object"}, "RNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProduct", "type": "object"}, "RNAProductIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference RNA", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProductIsoform", "type": "object"}, "ReactionDirectionEnum": {"description": "", "enum": ["left_to_right", "right_to_left", "bidirectional", "neutral"], "title": "ReactionDirectionEnum", "type": "string"}, "ReactionSideEnum": {"description": "", "enum": ["left", "right"], "title": "ReactionSideEnum", "type": "string"}, "ReactionToCatalystAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToCatalystAssociation", "type": "object"}, "ReactionToParticipantAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToParticipantAssociation", "type": "object"}, "ReagentTargetedGene": {"additionalProperties": false, "description": "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ReagentTargetedGene", "type": "object"}, "RegulatoryRegion": {"additionalProperties": false, "description": "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RegulatoryRegion", "type": "object"}, "RelationshipType": {"additionalProperties": false, "description": "An OWL property used as an edge label", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "RelationshipType", "type": "object"}, "RelativeFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a relative frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RelativeFrequencyAnalysisResult", "type": "object"}, "ResourceRoleEnum": {"description": "The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience.", "enum": ["primary_knowledge_source", "aggregator_knowledge_source", "supporting_data_source"], "title": "ResourceRoleEnum", "type": "string"}, "RetrievalSource": {"additionalProperties": false, "description": "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "resource_id": {"description": "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", "type": "string"}, "resource_role": {"$ref": "#/$defs/ResourceRoleEnum", "description": "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge."}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "upstream_resource_ids": {"description": "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["resource_id", "resource_role", "id", "category"], "title": "RetrievalSource", "type": "object"}, "SequenceAssociation": {"additionalProperties": false, "description": "An association between a sequence feature and a nucleic acid entity it is localized to.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceAssociation", "type": "object"}, "SequenceEnum": {"description": "type of sequence", "enum": ["na", "aa"], "title": "SequenceEnum", "type": "string"}, "SequenceFeatureRelationship": {"additionalProperties": false, "description": "For example, a particular exon is part of a particular transcript or gene", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceFeatureRelationship", "type": "object"}, "SequenceVariant": {"additionalProperties": false, "description": "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "The state of the sequence w.r.t a reference sequence", "type": "string"}, "has_gene": {"description": "Each allele can be associated with any number of genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SequenceVariant", "type": "object"}, "Serial": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Serials (journals) should have industry-standard identifier such as from ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "items": {"type": "string"}, "type": "array"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Serial", "type": "object"}, "SeverityValue": {"additionalProperties": false, "description": "describes the severity of a phenotypic feature or disease", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SeverityValue", "type": "object"}, "SiRNA": {"additionalProperties": false, "description": "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SiRNA", "type": "object"}, "SmallMolecule": {"additionalProperties": false, "description": "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SmallMolecule", "type": "object"}, "Snv": {"additionalProperties": false, "description": "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene": {"description": "connects an entity associated with one or more genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Snv", "type": "object"}, "SocioeconomicAttribute": {"additionalProperties": false, "description": "Attributes relating to a socioeconomic manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SocioeconomicAttribute", "type": "object"}, "SocioeconomicExposure": {"additionalProperties": false, "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category", "has_attribute"], "title": "SocioeconomicExposure", "type": "object"}, "SocioeconomicOutcome": {"additionalProperties": false, "description": "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event", "title": "SocioeconomicOutcome", "type": "object"}, "StrandEnum": {"description": "strand", "enum": ["+", "-", ".", "?"], "title": "StrandEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "a detailed investigation and/or analysis", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Study", "type": "object"}, "StudyPopulation": {"additionalProperties": false, "description": "A group of people banded together or treated as a group as participants in a research study.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyPopulation", "type": "object"}, "StudyVariable": {"additionalProperties": false, "description": "a variable that is used as a measure in the investigation of a study", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyVariable", "type": "object"}, "TaxonToTaxonAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between individuals of different taxa.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "TaxonToTaxonAssociation", "type": "object"}, "TaxonomicRank": {"additionalProperties": false, "description": "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "TaxonomicRank", "type": "object"}, "TextMiningResult": {"additionalProperties": false, "description": "A result of text mining.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "TextMiningResult", "type": "object"}, "Transcript": {"additionalProperties": false, "description": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Transcript", "type": "object"}, "TranscriptToGeneRelationship": {"additionalProperties": false, "description": "A gene is a collection of transcripts", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "TranscriptToGeneRelationship", "type": "object"}, "TranscriptionFactorBindingSite": {"additionalProperties": false, "description": "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "TranscriptionFactorBindingSite", "type": "object"}, "Treatment": {"additionalProperties": false, "description": "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_device": {"description": "connects an entity to one or more (medical) devices", "items": {"type": "string"}, "type": "array"}, "has_drug": {"description": "connects an entity to one or more drugs", "items": {"type": "string"}, "type": "array"}, "has_procedure": {"description": "connects an entity to one or more (medical) procedures", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Treatment", "type": "object"}, "VariantAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A variant that has a role in modeling the disease.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantAsAModelOfDiseaseAssociation", "type": "object"}, "VariantToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that variant", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the disease state", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToDiseaseAssociation", "type": "object"}, "VariantToGeneAssociation": {"additionalProperties": false, "description": "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneAssociation", "type": "object"}, "VariantToGeneExpressionAssociation": {"additionalProperties": false, "description": "An association between a variant and expression of a gene (i.e. e-QTL)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneExpressionAssociation", "type": "object"}, "VariantToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the phenotype state", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPhenotypicFeatureAssociation", "type": "object"}, "VariantToPopulationAssociation": {"additionalProperties": false, "description": "An association between a variant and a population, where the variant has particular frequency in the population", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number in object population that carry a particular allele, aka allele count", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", "type": "number"}, "has_total": {"description": "number all populations that carry a particular allele, aka allele number", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that is observed to have the frequency", "type": "string"}, "object_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "object_category_closure": {"description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_closure": {"description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_label_closure": {"description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "object_namespace": {"description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "retrieval_source_ids": {"description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "an allele that has a certain frequency in a given population", "type": "string"}, "subject_category": {"description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "subject_category_closure": {"description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_closure": {"description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_label_closure": {"description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": {"type": "string"}, "type": "array"}, "subject_namespace": {"description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"items": {"type": "string"}, "type": "array"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPopulationAssociation", "type": "object"}, "Virus": {"additionalProperties": false, "description": "A virus is a microorganism that replicates itself as a microRNA and infects the host cell.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Virus", "type": "object"}, "Zygosity": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"items": {"type": "string"}, "type": "array"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Zygosity", "type": "object"}}, "$id": "https://w3id.org/biolink/biolink-model", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": true, "metamodel_version": "1.7.0", "title": "Biolink-Model", "type": "object", "version": "3.2.5"}