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proper dashing on prefixmap
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sierra-moxon committed Oct 10, 2024
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -122,7 +122,7 @@ gen-project: $(PYMODEL)
--include python \
--include rdf \
-d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink_model_prefix_map.json
mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink-model-prefix-map.json
mv $(PYMODEL)/biolink*.py $(PYMODEL)/model.py
$(RUN) gen-pydantic src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py
$(RUN) gen-owl --mergeimports --no-metaclasses --no-type-objects --add-root-classes --mixins-as-expressions src/biolink_model/schema/biolink_model.yaml > $(DEST)/owl/biolink_model.owl.ttl
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2 changes: 1 addition & 1 deletion project/jsonld/biolink_model.context.jsonld
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@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2024-10-10T09:05:17",
"generation_date": "2024-10-10T09:15:55",
"source": "biolink_model.yaml"
},
"@context": {
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4 changes: 2 additions & 2 deletions project/jsonld/biolink_model.jsonld
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Expand Up @@ -35609,9 +35609,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "biolink_model.yaml",
"source_file_date": "2024-10-10T09:05:13",
"source_file_date": "2024-10-10T09:15:51",
"source_file_size": 400333,
"generation_date": "2024-10-10T09:05:20",
"generation_date": "2024-10-10T09:15:57",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/biolink_model.context.jsonld",
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5,656 changes: 2,828 additions & 2,828 deletions project/owl/biolink_model.owl.ttl
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262 changes: 262 additions & 0 deletions project/prefixmap/biolink-model-prefix-map.json
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{
"AGRKB": "https://www.alliancegenome.org/",
"APO": "http://purl.obolibrary.org/obo/APO_",
"AspGD": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=",
"BFO": "http://purl.obolibrary.org/obo/BFO_",
"BIGG.METABOLITE": "http://identifiers.org/bigg.metabolite/",
"BIGG.REACTION": "http://identifiers.org/bigg.reaction/",
"BIOGRID": "http://identifiers.org/biogrid/",
"BIOSAMPLE": "http://identifiers.org/biosample/",
"BSPO": "http://purl.obolibrary.org/obo/BSPO_",
"BTO": "http://purl.obolibrary.org/obo/BTO_",
"CAID": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=",
"CARO": "http://purl.obolibrary.org/obo/CARO_",
"CAS": "http://identifiers.org/cas/",
"CATH": "http://identifiers.org/cath/",
"CATH.SUPERFAMILY": "http://identifiers.org/cath.superfamily/",
"CDD": "http://identifiers.org/cdd/",
"CHADO": "http://gmod.org/wiki/Chado/",
"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
"CHEMBL.COMPOUND": "http://identifiers.org/chembl.compound/",
"CHEMBL.MECHANISM": "https://www.ebi.ac.uk/chembl/mechanism/inspect/",
"CHEMBL.TARGET": "http://identifiers.org/chembl.target/",
"CID": "http://pubchem.ncbi.nlm.nih.gov/compound/",
"CIO": "http://purl.obolibrary.org/obo/CIO_",
"CL": "http://purl.obolibrary.org/obo/CL_",
"CLINVAR": "http://identifiers.org/clinvar",
"CLO": "http://purl.obolibrary.org/obo/CLO_",
"COAR_RESOURCE": "http://purl.org/coar/resource_type/",
"COG": "https://www.ncbi.nlm.nih.gov/research/cog-project/",
"CPT": "https://www.ama-assn.org/practice-management/cpt/",
"CTD": "http://ctdbase.org/",
"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=",
"ChemBank": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=",
"ComplexPortal": "https://www.ebi.ac.uk/complexportal/complex/",
"DBSNP": "http://identifiers.org/dbsnp/",
"DDANAT": "http://purl.obolibrary.org/obo/DDANAT_",
"DGIdb": "https://www.dgidb.org/interaction_types",
"DOID": "http://purl.obolibrary.org/obo/DOID_",
"DOID-PROPERTY": "http://purl.obolibrary.org/obo/doid#",
"DRUGBANK": "http://identifiers.org/drugbank/",
"DrugCentral": "http://drugcentral.org/drugcard/",
"EC": "http://www.enzyme-database.org/query.php?ec=",
"ECO": "http://purl.obolibrary.org/obo/ECO_",
"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_",
"EGGNOG": "http://identifiers.org/eggnog/",
"EMAPA": "http://purl.obolibrary.org/obo/EMAPA_",
"ENSEMBL": "http://identifiers.org/ensembl/",
"ENVO": "http://purl.obolibrary.org/obo/ENVO_",
"ExO": "http://purl.obolibrary.org/obo/ExO_",
"FAO": "http://purl.obolibrary.org/obo/FAO_",
"FB": "http://identifiers.org/fb/",
"FBbt": "http://purl.obolibrary.org/obo/FBbt_",
"FBcv": "http://purl.obolibrary.org/obo/FBcv_",
"FBdv": "http://purl.obolibrary.org/obo/FBdv_",
"FMA": "http://purl.obolibrary.org/obo/FMA_",
"FOODON": "http://purl.obolibrary.org/obo/FOODON_",
"FYECO": "https://www.pombase.org/term/",
"FYPO": "http://purl.obolibrary.org/obo/FYPO_",
"GENEPIO": "http://purl.obolibrary.org/obo/GENEPIO_",
"GENO": "http://purl.obolibrary.org/obo/GENO_",
"GO": "http://purl.obolibrary.org/obo/GO_",
"GOLD.META": "http://identifiers.org/gold.meta/",
"GOP": "http://purl.obolibrary.org/obo/go#",
"GOREL": "http://purl.obolibrary.org/obo/GOREL_",
"GSID": "https://scholar.google.com/citations?user=",
"GTEx": "https://www.gtexportal.org/home/gene/",
"GTOPDB": "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=",
"HAMAP": "http://identifiers.org/hamap/",
"HANCESTRO": "http://www.ebi.ac.uk/ancestro/ancestro_",
"HCPCS": "http://purl.bioontology.org/ontology/HCPCS/",
"HGNC": "http://identifiers.org/hgnc/",
"HGNC.FAMILY": "http://identifiers.org/hgnc.family/",
"HMDB": "http://identifiers.org/hmdb/",
"HP": "http://purl.obolibrary.org/obo/HP_",
"HsapDv": "http://purl.obolibrary.org/obo/HsapDv_",
"IAO": "http://purl.obolibrary.org/obo/IAO_",
"ICD10": "https://icd.codes/icd9cm/",
"ICD9": "http://translator.ncats.nih.gov/ICD9_",
"IDO": "http://purl.obolibrary.org/obo/IDO_",
"INCHI": "http://identifiers.org/inchi/",
"INCHIKEY": "http://identifiers.org/inchikey/",
"INO": "http://purl.obolibrary.org/obo/INO_",
"INTACT": "http://identifiers.org/intact/",
"IUPHAR.FAMILY": "http://identifiers.org/iuphar.family/",
"KEGG": "http://www.kegg.jp/entry/",
"KEGG.BRITE": "https://bioregistry.io/kegg.brite:",
"KEGG.COMPOUND": "http://identifiers.org/kegg.compound/",
"KEGG.DISEASE": "http://identifiers.org/kegg.disease/",
"KEGG.DRUG": "http://identifiers.org/kegg.drug/",
"KEGG.ENVIRON": "http://identifiers.org/kegg.environ/",
"KEGG.GENES": "https://bioregistry.io/kegg.genes:bsu:",
"KEGG.GLYCAN": "http://identifiers.org/kegg.glycan/",
"KEGG.MODULE": "http://identifiers.org/kegg.module/",
"KEGG.ORTHOLOGY": "http://identifiers.org/kegg.orthology/",
"KEGG.PATHWAY": "https://bioregistry.io/kegg.pathway:",
"KEGG.RCLASS": "https://www.genome.jp/dbget-bin/www_bget?rc:",
"KEGG.REACTION": "http://identifiers.org/kegg.reaction/",
"LOINC": "http://loinc.org/rdf/",
"MA": "http://purl.obolibrary.org/obo/MA_",
"MAXO": "http://purl.obolibrary.org/obo/MAXO_",
"MEDDRA": "http://identifiers.org/meddra/",
"MESH": "http://id.nlm.nih.gov/mesh/",
"METANETX.REACTION": "https://www.metanetx.org/equa_info/",
"MGI": "http://identifiers.org/mgi/",
"MI": "http://purl.obolibrary.org/obo/MI_",
"MIR": "http://identifiers.org/mir/",
"MONDO": "http://purl.obolibrary.org/obo/MONDO_",
"MP": "http://purl.obolibrary.org/obo/MP_",
"MPATH": "http://purl.obolibrary.org/obo/MPATH_",
"MSigDB": "https://www.gsea-msigdb.org/gsea/msigdb/",
"MmusDv": "http://purl.obolibrary.org/obo/MMUSDV_",
"NBO": "http://purl.obolibrary.org/obo/NBO_",
"NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#",
"NCBIGene": "http://identifiers.org/ncbigene/",
"NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_",
"NCIT": "http://purl.obolibrary.org/obo/NCIT_",
"NCIT-OBO": "http://purl.obolibrary.org/obo/ncit#",
"NDC": "http://identifiers.org/ndc/",
"NDDF": "http://purl.bioontology.org/ontology/NDDF/",
"NLMID": "https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=",
"OBAN": "http://purl.org/oban/",
"OBI": "http://purl.obolibrary.org/obo/OBI_",
"OGMS": "http://purl.obolibrary.org/obo/OGMS_",
"OMIM": "http://purl.obolibrary.org/obo/OMIM_",
"OMIM.PS": "https://www.omim.org/phenotypicSeries/",
"OMIT": "http://purl.obolibrary.org/obo/OMIT_",
"ORCID": "https://orcid.org/",
"PANTHER.FAMILY": "http://www.pantherdb.org/panther/family.do?clsAccession=",
"PANTHER.PATHWAY": "http://identifiers.org/panther.pathway/",
"PATO": "http://purl.obolibrary.org/obo/PATO_",
"PCO": "http://purl.obolibrary.org/obo/PCO_",
"PFAM": "http://identifiers.org/pfam/",
"PHARMGKB.DISEASE": "https://www.pharmgkb.org/disease/",
"PHARMGKB.DRUG": "https://www.pharmgkb.org/chemical/",
"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",
"PIRSF": "http://identifiers.org/pirsf/",
"PMC": "http://europepmc.org/articles/PMC",
"PMCID": "http://www.ncbi.nlm.nih.gov/pmc/",
"PMID": "http://www.ncbi.nlm.nih.gov/pubmed/",
"PO": "http://purl.obolibrary.org/obo/PO_",
"PR": "http://purl.obolibrary.org/obo/PR_",
"PRINTS": "http://identifiers.org/prints/",
"PRODOM": "http://identifiers.org/prodom/",
"PROSITE": "http://identifiers.org/prosite/",
"PUBCHEM.COMPOUND": "http://identifiers.org/pubchem.compound/",
"PUBCHEM.SUBSTANCE": "http://identifiers.org/pubchem.substance/",
"PW": "http://purl.obolibrary.org/obo/PW_",
"PathWhiz": "http://smpdb.ca/pathways/#",
"PomBase": "https://www.pombase.org/gene/",
"REACT": "http://www.reactome.org/PathwayBrowser/#/",
"REPODB": "http://apps.chiragjpgroup.org/repoDB/",
"RFAM": "http://identifiers.org/rfam/",
"RGD": "http://identifiers.org/rgd/",
"RHEA": "http://identifiers.org/rhea/",
"RNACENTRAL": "http://identifiers.org/rnacentral/",
"RO": "http://purl.obolibrary.org/obo/RO_",
"RXCUI": "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=",
"RXNORM": "http://purl.bioontology.org/ontology/RXNORM/",
"ResearchID": "https://publons.com/researcher/",
"SEED.REACTION": "https://modelseed.org/biochem/reactions/",
"SEMMEDDB": "https://skr3.nlm.nih.gov/SemMedDB",
"SEPIO": "http://purl.obolibrary.org/obo/SEPIO_",
"SGD": "http://identifiers.org/sgd/",
"SIDER.DRUG": "http://identifiers.org/sider.drug/",
"SIO": "http://semanticscience.org/resource/SIO_",
"SMART": "http://identifiers.org/smart/",
"SMPDB": "http://identifiers.org/smpdb/",
"SNOMED": "http://purl.obolibrary.org/obo/SNOMED_",
"SNOMEDCT": "http://snomed.info/id/",
"SO": "http://purl.obolibrary.org/obo/SO_",
"SPDI": "https://api.ncbi.nlm.nih.gov/variation/v0/spdi/",
"STATO": "http://purl.obolibrary.org/obo/STATO_",
"STY": "http://purl.bioontology.org/ontology/STY/",
"SUPFAM": "http://identifiers.org/supfam/",
"ScopusID": "https://www.scopus.com/authid/detail.uri?authorId=",
"TAXRANK": "http://purl.obolibrary.org/obo/TAXRANK_",
"TCDB": "http://identifiers.org/tcdb/",
"TIGRFAM": "http://identifiers.org/tigrfam/",
"TO": "http://purl.obolibrary.org/obo/TO_",
"UBERGRAPH": "http://translator.renci.org/ubergraph-axioms.ofn#",
"UBERON": "http://purl.obolibrary.org/obo/UBERON_",
"UBERON_CORE": "http://purl.obolibrary.org/obo/uberon/core#",
"UBERON_NONAMESPACE": "http://purl.obolibrary.org/obo/core#",
"UMLS": "http://identifiers.org/umls/",
"UMLSSG": "https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt",
"UNII": "http://identifiers.org/unii/",
"UNIPROT.ISOFORM": "http://purl.uniprot.org/isoforms/",
"UO-PROPERTY": "http://purl.obolibrary.org/obo/uo#",
"UPHENO": "http://purl.obolibrary.org/obo/UPHENO_",
"UniProtKB": "http://purl.uniprot.org/uniprot/",
"VANDF": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/",
"VMC": "https://github.com/ga4gh/vr-spec/",
"WB": "http://identifiers.org/wb/",
"WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_",
"WBVocab": "http://bio2rdf.org/wormbase_vocabulary",
"WBbt": "http://purl.obolibrary.org/obo/WBbt_",
"WBls": "http://purl.obolibrary.org/obo/WBls_",
"WIKIDATA": "https://www.wikidata.org/entity/",
"WIKIDATA_PROPERTY": "https://www.wikidata.org/prop/",
"WIKIPATHWAYS": "http://identifiers.org/wikipathways/",
"WormBase": "https://www.wormbase.org/get?name=",
"XAO": "http://purl.obolibrary.org/obo/XAO_",
"XCO": "http://purl.obolibrary.org/obo/XCO_",
"XPO": "http://purl.obolibrary.org/obo/XPO_",
"Xenbase": "http://www.xenbase.org/gene/showgene.do?method=display&geneId=",
"ZFA": "http://purl.obolibrary.org/obo/ZFA_",
"ZFIN": "http://identifiers.org/zfin/",
"ZFS": "http://purl.obolibrary.org/obo/ZFS_",
"ZP": "http://purl.obolibrary.org/obo/ZP_",
"apollo": "https://github.com/GMOD/Apollo",
"biolink": "https://w3id.org/biolink/vocab/",
"bioschemas": "https://bioschemas.org/",
"dcat": "http://www.w3.org/ns/dcat#",
"dcid": "https://datacommons.org/browser/",
"dct": "http://purl.org/dc/terms/",
"dctypes": "http://purl.org/dc/dcmitype/",
"dictyBase": "http://dictybase.org/gene/",
"doi": "https://doi.org/",
"fabio": "http://purl.org/spar/fabio/",
"faldo": "http://biohackathon.org/resource/faldo#",
"foaf": "http://xmlns.com/foaf/0.1/",
"foodb.compound": "http://foodb.ca/compounds/",
"foodb.food": "http://foodb.ca/foods/",
"gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#",
"gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#",
"gtpo": "https://rdf.guidetopharmacology.org/ns/gtpo#",
"interpro": "https://www.ebi.ac.uk/interpro/entry/",
"isbn": "https://www.isbn-international.org/identifier/",
"isni": "https://isni.org/isni/",
"issn": "https://portal.issn.org/resource/ISSN/",
"linkml": "https://w3id.org/linkml/",
"medgen": "https://www.ncbi.nlm.nih.gov/medgen/",
"metacyc.reaction": "http://identifiers.org/metacyc.reaction:",
"mirbase": "http://identifiers.org/mirbase",
"mmmp.biomaps": "https://bioregistry.io/mmmp.biomaps:",
"ncats.bioplanet": "https://tripod.nih.gov/bioplanet/detail.jsp?pid=",
"ncats.drug": "https://drugs.ncats.io/drug/",
"oboInOwl": "http://www.geneontology.org/formats/oboInOwl#",
"orphanet": "http://www.orpha.net/ORDO/Orphanet_",
"os": "https://github.com/cmungall/owlstar/blob/master/owlstar.ttl",
"owl": "http://www.w3.org/2002/07/owl#",
"pav": "http://purl.org/pav/",
"prov": "http://www.w3.org/ns/prov#",
"qud": "http://qudt.org/1.1/schema/qudt#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"regulates": "http://example.org/UNKNOWN/regulates/",
"schema": "http://schema.org/",
"skos": "http://www.w3.org/2004/02/skos/core#",
"wgs": "http://www.w3.org/2003/01/geo/wgs84_pos",
"xsd": "http://www.w3.org/2001/XMLSchema#"
}
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