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biolink-model.yaml
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biolink-model.yaml
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id: https://w3id.org/biolink/biolink-model
name: Biolink-Model
description: Entity and association taxonomy and datamodel for life-sciences data
license: https://creativecommons.org/publicdomain/zero/1.0/
# Version should be kept in sync with primary Git repository release tag
version: 3.2.6
## ------------
##
## PREFIXES
## ------------
# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification
# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld
# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following
# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's
# which should ideally be repaired in one of the precedence lists.
#
# 1. The following 'prefixes:' delimited list has first precedence in resolution.
#
prefixes:
AGRKB: 'https://www.alliancegenome.org/'
apollo: 'https://github.com/GMOD/Apollo'
AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='
biolink: 'https://w3id.org/biolink/vocab/'
bioschemas: 'https://bioschemas.org/'
linkml: 'https://w3id.org/linkml/'
CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='
# Placeholder: just points to GMOD Chado wiki
CHADO: 'http://gmod.org/wiki/Chado/'
# Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve
ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='
CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'
CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'
CLINVAR: 'http://identifiers.org/clinvar'
COAR_RESOURCE: 'http://purl.org/coar/resource_type/'
COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'
ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/'
CPT: 'https://www.ama-assn.org/practice-management/cpt/'
CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='
CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='
CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='
CTD: 'http://ctdbase.org/'
DGIdb: 'https://www.dgidb.org/interaction_types'
dcat: 'http://www.w3.org/ns/dcat#'
dct: 'http://purl.org/dc/terms/'
dcid: 'https://datacommons.org/browser/'
doi: 'https://doi.org/'
DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'
DrugCentral: 'http://drugcentral.org/drugcard/'
ECTO: 'http://purl.obolibrary.org/obo/ECTO_'
EDAM-DATA: 'http://edamontology.org/data_'
EDAM-FORMAT: 'http://edamontology.org/format_'
EDAM-OPERATION: 'http://edamontology.org/operation_'
EDAM-TOPIC: 'http://edamontology.org/topic_'
EFO: 'http://www.ebi.ac.uk/efo/EFO_'
ExO: 'http://purl.obolibrary.org/obo/ExO_'
fabio: 'http://purl.org/spar/fabio/'
foaf: 'http://xmlns.com/foaf/0.1/'
foodb.food: 'http://foodb.ca/compounds/'
foodb.compound: 'http://foodb.ca/foods/'
FYECO: 'https://www.pombase.org/term/'
FYPO: 'http://purl.obolibrary.org/obo/FYPO_' # Fission Yeast Phenotype Ontology
gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'
GOREL: 'http://purl.obolibrary.org/obo/GOREL_'
# GOP: Gene Ontology Property (not really a GO term but an associated metadatum)
GOP: 'http://purl.obolibrary.org/obo/go#'
gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'
GSID: 'https://scholar.google.com/citations?user='
GTEx: 'https://www.gtexportal.org/home/gene/'
GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='
gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'
HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'
HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'
HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'
ICD10: 'https://icd.codes/icd9cm/'
ICD9: 'http://translator.ncats.nih.gov/ICD9_'
interpro: 'https://www.ebi.ac.uk/interpro/entry/'
INO: 'http://purl.obolibrary.org/obo/INO_'
isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international
isni: 'https://isni.org/isni/'
issn: 'https://portal.issn.org/resource/ISSN/'
ncats.drug: 'https://drugs.ncats.io/drug/'
KEGG.BRITE: 'http://www.kegg.jp/entry/'
KEGG.DGROUP: 'http://www.kegg.jp/entry/'
KEGG.ENZYME: 'http://www.kegg.jp/entry/'
KEGG.GENE: 'http://www.kegg.jp/entry/'
KEGG.PATHWAY: 'https://www.kegg.jp/entry/'
KEGG.RCLASS: 'http://www.kegg.jp/entry/'
LOINC: 'http://loinc.org/rdf/'
MAXO: 'http://purl.obolibrary.org/obo/MAXO_'
medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'
metacyc.reaction: 'http://identifiers.org/metacyc.reaction:'
METANETX.REACTION: 'https://www.metanetx.org/equa_info/'
MESH: 'http://id.nlm.nih.gov/mesh/'
MI: 'http://purl.obolibrary.org/obo/MI_'
mirbase: 'http://identifiers.org/mirbase'
mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'
MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'
MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'
NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'
ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='
NCBIGene: 'http://identifiers.org/ncbigene/'
NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'
NDDF: 'http://purl.bioontology.org/ontology/NDDF/'
NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='
OBAN: 'http://purl.org/oban/'
oboformat: 'http://www.geneontology.org/formats/oboInOwl#'
OMIM.PS: 'https://www.omim.org/phenotypicSeries/'
ORCID: 'https://orcid.org/'
orphanet: 'http://www.orpha.net/ORDO/Orphanet_'
os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'
PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='
PathWhiz: 'http://smpdb.ca/pathways/#' # See also https://smpdb.ca/pathwhiz/
pav: 'http://purl.org/pav/'
PHARMGKB.CHEMICAL: 'https://www.pharmgkb.org/chemical/'
PHARMGKB.DISEASE: 'https://www.pharmgkb.org/disease/'
PHARMGKB.GENE: 'https://www.pharmgkb.org/gene/'
PHARMGKB.PATHWAYS: 'https://www.pharmgkb.org/pathway/'
PHARMGKB.VARIANT: 'https://www.pharmgkb.org/variant/'
PHAROS: 'http://pharos.nih.gov'
PomBase: 'https://www.pombase.org/gene/'
prov: 'http://www.w3.org/ns/prov#'
qud: 'http://qudt.org/1.1/schema/qudt#'
REPODB: 'http://apps.chiragjpgroup.org/repoDB/'
ResearchID: 'https://publons.com/researcher/'
RO: 'http://purl.obolibrary.org/obo/RO_'
RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'
RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='
schema: 'http://schema.org/'
ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='
SEED.REACTION: 'https://modelseed.org/biochem/reactions/'
SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'
SIO: 'http://semanticscience.org/resource/SIO_'
SNOMEDCT: 'http://snomed.info/id/'
SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'
UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'
UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'
UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'
# The UMLS Semantic types and groups namespaces don't have a directly
# resolvable Base URI, but we point to a pair of sensible web documents
STY: 'http://purl.bioontology.org/ontology/STY/'
UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'
UniProtKB: 'http://purl.uniprot.org/uniprot/'
UNIPROT.ISOFORM: 'http://purl.uniprot.org/isoforms/'
VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'
UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'
# The "Variation Modelling Collaboration" (VMC) is not (yet) a conventional namespace so we point to its Github repo
# See also: https://www.ga4gh.org/work_stream/genomic-knowledge-standards/#existing-standards and
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153148/
VMC: 'https://github.com/ga4gh/vr-spec/'
WBls: 'http://purl.obolibrary.org/obo/WBBL_'
WBbt: 'http://purl.obolibrary.org/obo/WBBT_'
WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'
WIKIDATA: 'https://www.wikidata.org/wiki/' # Wikidata Entity
WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:' # Wikidata Property - not a conventional namespace prefix
wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'
XPO: 'http://purl.obolibrary.org/obo/XPO_' # Xenopus Phenotype Ontology
Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='
default_prefix: biolink
default_range: string
# 2. The following prefix maps are retrieved from the
# specified contexts defined at https://prefixcommons.org/
default_curi_maps:
- obo_context
- idot_context
- monarch_context
- semweb_context
# The following 'standard' prefixes are also used.
emit_prefixes:
- rdf
- rdfs
- xsd
- skos
- OIO
- BIOGRID
- SO
## ------------
## SUBSETS
## ------------
subsets:
model_organism_database:
description: >-
Subset that is relevant for a typical Model Organism Database (MOD)
translator_minimal:
description: >-
Minimum subset of translator work
samples:
description: >-
Sample/biosample datamodel
testing:
description: >-
TBD
## ------------
## TYPES
## ------------
imports:
- linkml:types
types:
chemical formula value:
uri: xsd:string
base: str
description: A chemical formula
notes:
- Should be implemented as a stronger type
category type:
typeof: uriorcurie
description: >-
A primitive type in which the value denotes a class within the biolink model.
The value must be a URI or a CURIE. In a Neo4j representation, the value should
be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation,
the value should be a URI such as https://w3id.org/biolink/vocab/Gene
iri type:
typeof: uriorcurie
description: >-
An IRI
label type:
typeof: string
description: >-
A string that provides a human-readable name for an entity
predicate type:
typeof: uriorcurie
description: >-
A CURIE from the biolink related_to hierarchy.
For example, biolink:related_to, biolink:causes, biolink:treats.
narrative text:
typeof: string
description: >-
A string that provides a human-readable description of something
symbol type:
typeof: string
frequency value:
typeof: string
uri: UO:0000105
percentage frequency value:
typeof: double
uri: UO:0000187
quotient:
aliases: [ 'ratio' ]
typeof: double
uri: UO:0010006
unit:
typeof: string
uri: UO:0000000
id_prefixes:
- UO
exact_mappings:
- qud:Unit
time type:
typeof: time
biological sequence:
typeof: string
## ------------
## SLOTS
## ------------
slots:
## ---------------
## ATTRIBUTE SLOTS
## ---------------
has attribute:
description: >-
connects any entity to an attribute
domain: entity
range: attribute
multivalued: true
in_subset:
- samples
close_mappings:
# RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'
- OBI:0001927
exact_mappings:
- SIO:000008
narrow_mappings:
# if 'has attribute' annotates a NamedThing as subject or
# object of an association, these OBAN mappings may apply
- OBAN:association_has_subject_property
- OBAN:association_has_object_property
- CPT:has_possibly_included_panel_element
- DRUGBANK:category
# RTX contributed terms. Could perhaps review for more semantically precise mappings?
- EFO:is_executed_in
- HANCESTRO:0301
- LOINC:has_action_guidance
- LOINC:has_adjustment
- LOINC:has_aggregation_view
- LOINC:has_approach_guidance
- LOINC:has_divisor
- LOINC:has_exam
- LOINC:has_method
- LOINC:has_modality_subtype
- LOINC:has_object_guidance
- LOINC:has_scale
- LOINC:has_suffix
- LOINC:has_time_aspect
- LOINC:has_time_modifier
- LOINC:has_timing_of
# disease is stage
- NCIT:R88
- NCIT:eo_disease_has_property_or_attribute
- NCIT:has_data_element
- NCIT:has_pharmaceutical_administration_method
- NCIT:has_pharmaceutical_basic_dose_form
- NCIT:has_pharmaceutical_intended_site
- NCIT:has_pharmaceutical_release_characteristics
- NCIT:has_pharmaceutical_state_of_matter
- NCIT:has_pharmaceutical_transformation
- NCIT:is_qualified_by
- NCIT:qualifier_applies_to
- NCIT:role_has_domain
- NCIT:role_has_range
- INO:0000154
- HANCESTRO:0308
- OMIM:has_inheritance_type
- orphanet:C016
- orphanet:C017
- RO:0000053
# RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here
- RO:0000086
- RO:0000087
- SNOMED:has_access
- SNOMED:has_clinical_course
- SNOMED:has_count_of_base_of_active_ingredient
- SNOMED:has_dose_form_administration_method
- SNOMED:has_dose_form_release_characteristic
- SNOMED:has_dose_form_transformation
- SNOMED:has_finding_context
- SNOMED:has_finding_informer
- SNOMED:has_inherent_attribute
- SNOMED:has_intent
- SNOMED:has_interpretation
- SNOMED:has_laterality
- SNOMED:has_measurement_method
- SNOMED:has_method
- SNOMED:has_priority
- SNOMED:has_procedure_context
- SNOMED:has_process_duration
- SNOMED:has_property
- SNOMED:has_revision_status
- SNOMED:has_scale_type
- SNOMED:has_severity
- SNOMED:has_specimen
- SNOMED:has_state_of_matter
- SNOMED:has_subject_relationship_context
- SNOMED:has_surgical_approach
- SNOMED:has_technique
- SNOMED:has_temporal_context
- SNOMED:has_time_aspect
- SNOMED:has_units
- UMLS:has_structural_class
- UMLS:has_supported_concept_property
- UMLS:has_supported_concept_relationship
- UMLS:may_be_qualified_by
has attribute type:
description: >-
connects an attribute to a class that describes it
domain: attribute
range: ontology class
multivalued: false
required: true
in_subset:
- samples
narrow_mappings:
- LOINC:has_modality_type
- LOINC:has_view_type
# TRAPI Attribute schema alignment:
# value: NamedThing.name
# value_type: NamedThing.category
# value_type_name: quantity_value.NamedThing.name
has qualitative value:
description: >-
connects an attribute to a value
domain: attribute
range: named thing
multivalued: false
in_subset:
- samples
# TRAPI Attribute schema alignment:
# value: quantity_value.has_numeric_value[double] - may be a vector?
# value_type: quantity_value.has_unit.unit.uri
# value_type_name: quantity_value.has_unit.unit.name[string]
has quantitative value:
description: >-
connects an attribute to a value
domain: attribute
range: quantity value
multivalued: true
exact_mappings:
- qud:quantityValue
narrow_mappings:
- SNOMED:has_concentration_strength_numerator_value
- SNOMED:has_presentation_strength_denominator_value
- SNOMED:has_presentation_strength_numerator_value
in_subset:
- samples
has numeric value:
description: >-
connects a quantity value to a number
domain: quantity value
range: double
multivalued: false
exact_mappings:
- qud:quantityValue
in_subset:
- samples
has unit:
description: >-
connects a quantity value to a unit
domain: quantity value
range: unit
multivalued: false
close_mappings:
# These RTX contributed terms mean "is unit of" which is the semantic inverse of this biolink:has_unit term
- EFO:0001697
- UO-PROPERTY:is_unit_of
exact_mappings:
- qud:unit
- IAO:0000039
narrow_mappings:
- SNOMED:has_concentration_strength_denominator_unit
- SNOMED:has_concentration_strength_numerator_unit
- SNOMED:has_presentation_strength_denominator_unit
- SNOMED:has_presentation_strength_numerator_unit
- SNOMED:has_unit_of_presentation
in_subset:
- samples
base coordinate:
is_a: sequence localization attribute
aliases: [ 'one-based', 'fully-closed' ]
description: >-
A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.
range: integer
## --------------------
## NODE PROPERTY SLOTS
## --------------------
node property:
description: >-
A grouping for any property that holds between a node and a value
domain: named thing
id:
identifier: true
domain: entity
description: >-
A unique identifier for an entity.
Must be either a CURIE shorthand for a URI or a complete URI
in_subset:
- translator_minimal
required: true
exact_mappings:
- AGRKB:primaryId
- gff3:ID
- gpi:DB_Object_ID
iri:
description: >-
An IRI for an entity. This is determined by the id using expansion rules.
range: iri type
in_subset:
- translator_minimal
- samples
exact_mappings:
- WIKIDATA_PROPERTY:P854
type:
slot_uri: rdf:type
domain: entity
exact_mappings:
- AGRKB:soTermId
- gff3:type
- gpi:DB_Object_Type
multivalued: true
category:
is_a: type
domain: entity
range: category type
designates_type: true
description: >-
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the
biolink entity type class.
* In a neo4j database this MAY correspond to the neo4j label tag.
* In an RDF database it should be a biolink model class URI.
This field is multi-valued. It should include values for ancestors of the biolink class; for example,
a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...
In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink
class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`
may have a rdf:type assertion to a SO class such as TF_binding_site,
which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,
biolink:MolecularEntity, biolink:NamedThing}
is_class_field: true
multivalued: true
in_subset:
- translator_minimal
publication type:
slot_uri: dct:type
description: >-
Ontology term for publication type may be drawn from
Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),
FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),
the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),
the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres
(http://vocabularies.coar-repositories.org/documentation/resource_types/),
Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or
equivalent publication type ontology. When a given publication type ontology term
is used within a given knowledge graph, then the CURIE identified term must be
documented in the graph as a concept node of biolink:category biolink:OntologyClass.
values_from: # Not sure which takes precedence, if any...
- dctypes
- fabio
- MESH_PUB
- COAR_RESOURCE
- WIKIDATA
name:
aliases: [ 'label', 'display name', 'title' ]
description: >-
A human-readable name for an attribute or entity.
domain: entity
range: label type
in_subset:
- translator_minimal
- samples
slot_uri: rdfs:label
exact_mappings:
- gff3:Name
- gpi:DB_Object_Name
narrow_mappings:
- dct:title
- WIKIDATA_PROPERTY:P1476
stoichiometry:
description: >-
the relationship between the relative quantities of substances taking part in a reaction or
forming a compound, typically a ratio of whole integers.
is_a: association slot
range: integer
reaction direction:
description: >-
the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)
is_a: association slot
range: ReactionDirectionEnum
narrow_mappings:
- NCIT:C42677
reaction balanced:
is_a: association slot
range: boolean
reaction side:
description: >-
the side of a reaction being modeled (ie: left or right)
is_a: association slot
range: ReactionSideEnum
symbol:
is_a: node property
domain: named thing
description: >-
Symbol for a particular thing
exact_mappings:
- AGRKB:symbol
- gpi:DB_Object_Symbol
synonym:
is_a: node property
aliases: [ 'alias' ]
domain: named thing
range: label type
description: >-
Alternate human-readable names for a thing
multivalued: true
in_subset:
- translator_minimal
narrow_mappings:
# there is an interesting debate here: are these terms "narrower" a.k.a. more specialized instances of
# 'biolink:synonym' or should they be binned into their respective namesake class of mappings?
# namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.
- skos:altLabel
- gff3:Alias
- AGRKB:synonyms
- gpi:DB_Object_Synonyms
# TODO: RTX contributed terms mapped here... May need review?
- HANCESTRO:0330
- IAO:0000136
- RXNORM:has_tradename
exact synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasExactSynonym
broad synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasBroadSynonym
narrow synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasNarrowSynonym
related synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasRelatedSynonym
has topic:
aliases: [ 'topic', 'descriptors' ]
is_a: node property
range: ontology class
exact_mappings:
- foaf:topic
description: >-
Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.
See https://github.com/biolink/biolink-model/issues/238
xref:
aliases: [ 'dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls' ]
domain: named thing
range: uriorcurie
description: >-
Alternate CURIEs for a thing
multivalued: true
in_subset:
- translator_minimal
narrow_mappings:
- gff3:Dbxref
- gpi:DB_Xrefs
support graphs:
description: >-
A list of knowledge graphs that support the existence of this node.
multivalued: true
in_subset:
- translator_minimal
resource id:
is_a: node property
description: >-
The CURIE for an Information Resource that served as a source
of knowledge expressed in an Edge, or a source of data used to
generate this knowledge.
domain: retrieval source
range: uriorcurie
in_subset:
- translator_minimal
resource role:
is_a: node property
description: >-
The role played by the InformationResource in serving as a
source for an Edge. Note that a given Edge should have one
and only one 'primary' source, and may have any number of
'aggregator' or 'supporting data' sources.
domain: retrieval source
range: ResourceRoleEnum
in_subset:
- translator_minimal
retrieval source ids:
description: >-
A list of retrieval sources that served as a source of knowledge
expressed in an Edge, or a source of data used to generate this
knowledge.
multivalued: true
range: retrieval source
in_subset:
- translator_minimal
full name:
is_a: node property
domain: named thing
range: label type
description: >-
a long-form human readable name for a thing
upstream resource ids:
is_a: node property
description: >-
An upstream InformationResource from which the resource
being described directly retrieved a record of the knowledge
expressed in the Edge, or data used to generate this knowledge.
This is an array because there are cases where a merged Edge
holds knowledge that was retrieved from multiple sources. e.g.
an Edge provided by the ARAGORN ARA can expressing knowledge it
retrieved from both the automat-mychem-info and molepro KPs,
which both provided it with records of this single fact.
domain: retrieval source
range: uriorcurie
description:
aliases: [ 'definition' ]
range: narrative text
description: >-
a human-readable description of an entity
in_subset:
- translator_minimal
slot_uri: dct:description
exact_mappings:
- IAO:0000115
- skos:definitions
narrow_mappings:
- gff3:Description
systematic synonym:
is_a: node property
domain: named thing
range: label type
multivalued: true
slot_uri: GOP:systematic_synonym
description: >-
more commonly used for gene symbols in yeast
affiliation:
is_a: node property
description: >-
a professional relationship between one provider (often a person) within another provider (often an organization).
Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.
domain: agent
range: uriorcurie
multivalued: true
address:
is_a: node property
description: >-
the particulars of the place where someone or an organization is situated. For now, this slot is a
simple text "blob" containing all relevant details of the given location for fitness of purpose.
For the moment, this "address" can include other contact details such as email and phone number(?).
## Space
latitude:
is_a: node property
range: float
description: >-
latitude
exact_mappings:
- wgs:lat
longitude:
is_a: node property
range: float
description: >-
longitude
exact_mappings:
- wgs:long
## Time
timepoint:
aliases: [ 'duration' ]
range: time type
description: >-
a point in time
creation date:
is_a: node property
aliases: [ 'publication date' ]
range: date
description: >-
date on which an entity was created. This can be applied to nodes or edges
exact_mappings:
- dct:createdOn
- WIKIDATA_PROPERTY:P577
update date:
is_a: node property
range: date
description: >-
date on which an entity was updated. This can be applied to nodes or edges
## Statistics
aggregate statistic:
is_a: node property
abstract: true
has count:
description: >-
number of things with a particular property
is_a: aggregate statistic
range: integer
exact_mappings:
- LOINC:has_count
has total:
description: >-
total number of things in a particular reference set
is_a: aggregate statistic
range: integer
has quotient:
is_a: aggregate statistic
range: double
has percentage:
description: >-
equivalent to has quotient multiplied by 100
is_a: aggregate statistic
range: double
## Properties for Information Content Entity and Publication Nodes
has taxonomic rank:
is_a: node property
range: taxonomic rank
multivalued: false
mappings:
- WIKIDATA:P105
has dataset:
is_a: node property
domain: dataset version
range: dataset
slot_uri: dct:source
source web page:
is_a: node property
domain: dataset summary
broad_mappings:
- dct:source
source logo:
is_a: node property
domain: dataset summary
slot_uri: schema:logo
retrieved on:
is_a: node property
domain: dataset
range: date
exact_mappings:
- pav:retrievedOn
version of:
is_a: node property
domain: dataset version
range: dataset summary
exact_mappings:
- dct:isVersionOf
version:
is_a: node property
domain: dataset
broad_mappings:
- pav:version
- owl:versionInfo
license:
is_a: node property
domain: information content entity
exact_mappings:
- dct:license
narrow_mappings:
- WIKIDATA_PROPERTY:P275
rights:
is_a: node property
domain: information content entity
exact_mappings:
- dct:rights
format:
is_a: node property
domain: information content entity
exact_mappings:
- dct:format
- WIKIDATA_PROPERTY:P2701
created with:
is_a: node property
domain: dataset
exact_mappings:
- pav:createdWith
download url:
is_a: node property
domain: information content entity
slot_uri: dcat:downloadURL
dataset download url:
is_a: node property
domain: dataset
slot_uri: dcat:downloadURL
distribution download url:
is_a: node property
domain: dataset distribution
exact_mappings:
- dcat:downloadURL
ingest date:
is_a: node property
domain: dataset version
slot_uri: pav:version
has distribution:
is_a: node property
domain: dataset version
range: dataset distribution
slot_uri: dct:distribution
published in:
is_a: node property
description: >-
CURIE identifier of a broader publication context within which the publication may be placed,
e.g. a specified book or journal.
domain: publication
range: uriorcurie
values_from:
- NLMID
- issn
- isbn
exact_mappings:
- WIKIDATA_PROPERTY:P1433
iso abbreviation:
is_a: node property
description: >-
Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system
See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,
then the iso abbreviation pertains to the broader publication context (the journal) within which the given
publication node is embedded, not the publication itself.
domain: publication
exact_mappings:
- WIKIDATA_PROPERTY:P1160
authors:
is_a: node property
singular_name: author
description: >-
connects an publication to the list of authors who contributed to the publication.
This property should be a comma-delimited list of author names. It is recommended that an author's name
be formatted as "surname, firstname initial.". Note that this property is a node annotation expressing
the citation list of authorship which might typically otherwise be more completely documented in
biolink:PublicationToProviderAssociation defined edges which point to full details about an author
and possibly, some qualifiers which clarify the specific status of a given author in the publication.
multivalued: true
domain: publication
volume:
is_a: node property
description: >-
volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication
domain: publication
exact_mappings:
- WIKIDATA_PROPERTY:P478
chapter:
is_a: node property
description: >-
chapter of a book
domain: book chapter
exact_mappings:
- WIKIDATA:Q1980247