From 632f86ea296803c481f76001a7936f85d00029dd Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 20 May 2021 14:29:40 -0700 Subject: [PATCH 1/5] fix NCBIGene for biolink-model --- registry/idot_context.jsonld | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/registry/idot_context.jsonld b/registry/idot_context.jsonld index d7777ca..2b372f8 100644 --- a/registry/idot_context.jsonld +++ b/registry/idot_context.jsonld @@ -484,7 +484,7 @@ "NONCODEV4.GENE": "http://identifiers.org/noncodev4.gene/", "WIKIGENES": "http://identifiers.org/wikigenes/", "GWASCENTRAL.STUDY": "http://identifiers.org/gwascentral.study/", - "NCBIGENE": "http://identifiers.org/ncbigene/", + "NCBIGene": "http://identifiers.org/ncbigene/", "GRID": "http://identifiers.org/grid/", "MP": "http://identifiers.org/mp/", "SIDER.EFFECT": "http://identifiers.org/sider.effect/", From a0255f1babcf3a882d3e817131d005a270e1a469 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 21 May 2021 08:32:55 -0700 Subject: [PATCH 2/5] update obo_context --- registry/obo_context.jsonld | 1996 +++++++++++++++++++++++++++++++---- 1 file changed, 1791 insertions(+), 205 deletions(-) diff --git a/registry/obo_context.jsonld b/registry/obo_context.jsonld index 6f79ea8..5afcf51 100644 --- a/registry/obo_context.jsonld +++ b/registry/obo_context.jsonld @@ -1,205 +1,1791 @@ -{ - "@context": { - "AAO": "http://purl.obolibrary.org/obo/AAO_", - "ADW": "http://purl.obolibrary.org/obo/ADW_", - "AEO": "http://purl.obolibrary.org/obo/AEO_", - "AERO": "http://purl.obolibrary.org/obo/AERO_", - "AGRO": "http://purl.obolibrary.org/obo/AGRO_", - "APO": "http://purl.obolibrary.org/obo/APO_", - "ARO": "http://purl.obolibrary.org/obo/ARO_", - "ATO": "http://purl.obolibrary.org/obo/ATO_", - "BCGO": "http://purl.obolibrary.org/obo/BCGO_", - "BCO": "http://purl.obolibrary.org/obo/BCO_", - "BFO": "http://purl.obolibrary.org/obo/BFO_", - "BILA": "http://purl.obolibrary.org/obo/BILA_", - "BOOTSTREP": "http://purl.obolibrary.org/obo/BOOTSTREP_", - "BSPO": "http://purl.obolibrary.org/obo/BSPO_", - "BTO": "http://purl.obolibrary.org/obo/BTO_", - "CARO": "http://purl.obolibrary.org/obo/CARO_", - "CDAO": "http://purl.obolibrary.org/obo/CDAO_", - "CEPH": "http://purl.obolibrary.org/obo/CEPH_", - "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", - "CHEMINF": "http://purl.obolibrary.org/obo/CHEMINF_", - "CHMO": "http://purl.obolibrary.org/obo/CHMO_", - "CIO": "http://purl.obolibrary.org/obo/CIO_", - "CL": "http://purl.obolibrary.org/obo/CL_", - "CLO": "http://purl.obolibrary.org/obo/CLO_", - "CMF": "http://purl.obolibrary.org/obo/CMF_", - "CMO": "http://purl.obolibrary.org/obo/CMO_", - "CRO": "http://purl.obolibrary.org/obo/CRO_", - "CTENO": "http://purl.obolibrary.org/obo/CTENO_", - "CVDO": "http://purl.obolibrary.org/obo/CVDO_", - "DC_CL": "http://purl.obolibrary.org/obo/DC_CL_", - "DDANAT": "http://purl.obolibrary.org/obo/DDANAT_", - "DDPHENO": "http://purl.obolibrary.org/obo/DDPHENO_", - "DIDEO": "http://purl.obolibrary.org/obo/DIDEO_", - "DINTO": "http://purl.obolibrary.org/obo/DINTO_", - "DOID": "http://purl.obolibrary.org/obo/DOID_", - "DRON": "http://purl.obolibrary.org/obo/DRON_", - "DUO": "http://purl.obolibrary.org/obo/DUO_", - "ECO": "http://purl.obolibrary.org/obo/ECO_", - "ECOCORE": "http://purl.obolibrary.org/obo/ECOCORE_", - "EHDA": "http://purl.obolibrary.org/obo/EHDA_", - "EHDAA": "http://purl.obolibrary.org/obo/EHDAA_", - "EHDAA2": "http://purl.obolibrary.org/obo/EHDAA2_", - "EMAP": "http://purl.obolibrary.org/obo/EMAP_", - "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", - "ENVO": "http://purl.obolibrary.org/obo/ENVO_", - "EO": "http://purl.obolibrary.org/obo/EO_", - "EPO": "http://purl.obolibrary.org/obo/EPO_", - "ERO": "http://purl.obolibrary.org/obo/ERO_", - "EUPATH": "http://purl.obolibrary.org/obo/EUPATH_", - "EV": "http://purl.obolibrary.org/obo/EV_", - "EXO": "http://purl.obolibrary.org/obo/EXO_", - "FAO": "http://purl.obolibrary.org/obo/FAO_", - "FBSP": "http://purl.obolibrary.org/obo/FBSP_", - "FBbi": "http://purl.obolibrary.org/obo/FBbi_", - "FBbt": "http://purl.obolibrary.org/obo/FBbt_", - "FBcv": "http://purl.obolibrary.org/obo/FBcv_", - "FBdv": "http://purl.obolibrary.org/obo/FBdv_", - "FIX": "http://purl.obolibrary.org/obo/FIX_", - "FLOPO": "http://purl.obolibrary.org/obo/FLOPO_", - "FLU": "http://purl.obolibrary.org/obo/FLU_", - "FMA": "http://purl.obolibrary.org/obo/FMA_", - "FOODON": "http://purl.obolibrary.org/obo/FOODON_", - "FYPO": "http://purl.obolibrary.org/obo/FYPO_", - "GAZ": "http://purl.obolibrary.org/obo/GAZ_", - "GENEPIO": "http://purl.obolibrary.org/obo/GENEPIO_", - "GENO": "http://purl.obolibrary.org/obo/GENO_", - "GEO": "http://purl.obolibrary.org/obo/GEO_", - "GO": "http://purl.obolibrary.org/obo/GO_", - "GRO": "http://purl.obolibrary.org/obo/GRO_", - "HABRONATTUS": "http://purl.obolibrary.org/obo/HABRONATTUS_", - "HAO": "http://purl.obolibrary.org/obo/HAO_", - "HOM": "http://purl.obolibrary.org/obo/HOM_", - "HP": "http://purl.obolibrary.org/obo/HP_", - "HSAPDV": "http://purl.obolibrary.org/obo/HSAPDV_", - "IAO": "http://purl.obolibrary.org/obo/IAO_", - "ICO": "http://purl.obolibrary.org/obo/ICO_", - "IDO": "http://purl.obolibrary.org/obo/IDO_", - "IDOMAL": "http://purl.obolibrary.org/obo/IDOMAL_", - "IEV": "http://purl.obolibrary.org/obo/IEV_", - "IMR": "http://purl.obolibrary.org/obo/IMR_", - "IPR": "http://purl.obolibrary.org/obo/IPR_", - "KISAO": "http://purl.obolibrary.org/obo/KISAO_", - "LIPRO": "http://purl.obolibrary.org/obo/LIPRO_", - "LOGGERHEAD": "http://purl.obolibrary.org/obo/LOGGERHEAD_", - "MA": "http://purl.obolibrary.org/obo/MA_", - "MAMO": "http://purl.obolibrary.org/obo/MAMO_", - "MAO": "http://purl.obolibrary.org/obo/MAO_", - "MAT": "http://purl.obolibrary.org/obo/MAT_", - "MF": "http://purl.obolibrary.org/obo/MF_", - "MFMO": "http://purl.obolibrary.org/obo/MFMO_", - "MFO": "http://purl.obolibrary.org/obo/MFO_", - "MFOEM": "http://purl.obolibrary.org/obo/MFOEM_", - "MFOMD": "http://purl.obolibrary.org/obo/MFOMD_", - "MI": "http://purl.obolibrary.org/obo/MI_", - "MIAPA": "http://purl.obolibrary.org/obo/MIAPA_", - "MICRO": "http://purl.obolibrary.org/obo/MICRO_", - "MIRNAO": "http://purl.obolibrary.org/obo/MIRNAO_", - "MIRO": "http://purl.obolibrary.org/obo/MIRO_", - "MMO": "http://purl.obolibrary.org/obo/MMO_", - "MMUSDV": "http://purl.obolibrary.org/obo/MMUSDV_", - "MO": "http://purl.obolibrary.org/obo/MO_", - "MOD": "http://purl.obolibrary.org/obo/MOD_", - "MONDO": "http://purl.obolibrary.org/obo/MONDO_", - "MOP": "http://purl.obolibrary.org/obo/MOP_", - "MP": "http://purl.obolibrary.org/obo/MP_", - "MPATH": "http://purl.obolibrary.org/obo/MPATH_", - "MPIO": "http://purl.obolibrary.org/obo/MPIO_", - "MRO": "http://purl.obolibrary.org/obo/MRO_", - "MS": "http://purl.obolibrary.org/obo/MS_", - "NBO": "http://purl.obolibrary.org/obo/NBO_", - "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "NCRO": "http://purl.obolibrary.org/obo/NCRO_", - "NIF_CELL": "http://purl.obolibrary.org/obo/NIF_CELL_", - "NIF_DYSFUNCTION": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_", - "NIF_GROSSANATOMY": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_", - "NMR": "http://purl.obolibrary.org/obo/NMR_", - "OAE": "http://purl.obolibrary.org/obo/OAE_", - "OARCS": "http://purl.obolibrary.org/obo/OARCS_", - "OBA": "http://purl.obolibrary.org/obo/OBA_", - "OBCS": "http://purl.obolibrary.org/obo/OBCS_", - "OBI": "http://purl.obolibrary.org/obo/OBI_", - "OBIB": "http://purl.obolibrary.org/obo/OBIB_", - "OBO_REL": "http://purl.obolibrary.org/obo/OBO_REL_", - "OGG": "http://purl.obolibrary.org/obo/OGG_", - "OGI": "http://purl.obolibrary.org/obo/OGI_", - "OGMS": "http://purl.obolibrary.org/obo/OGMS_", - "OGSF": "http://purl.obolibrary.org/obo/OGSF_", - "OHD": "http://purl.obolibrary.org/obo/OHD_", - "OHMI": "http://purl.obolibrary.org/obo/OHMI_", - "OLATDV": "http://purl.obolibrary.org/obo/OLATDV_", - "OMIABIS": "http://purl.obolibrary.org/obo/OMIABIS_", - "OMIT": "http://purl.obolibrary.org/obo/OMIT_", - "OMP": "http://purl.obolibrary.org/obo/OMP_", - "OMRSE": "http://purl.obolibrary.org/obo/OMRSE_", - "ONTONEO": "http://purl.obolibrary.org/obo/ONTONEO_", - "OOSTT": "http://purl.obolibrary.org/obo/OOSTT_", - "OPL": "http://purl.obolibrary.org/obo/OPL_", - "OVAE": "http://purl.obolibrary.org/obo/OVAE_", - "PAO": "http://purl.obolibrary.org/obo/PAO_", - "PATO": "http://purl.obolibrary.org/obo/PATO_", - "PCO": "http://purl.obolibrary.org/obo/PCO_", - "PDRO": "http://purl.obolibrary.org/obo/PDRO_", - "PDUMDV": "http://purl.obolibrary.org/obo/PDUMDV_", - "PD_ST": "http://purl.obolibrary.org/obo/PD_ST_", - "PECO": "http://purl.obolibrary.org/obo/PECO_", - "PGDSO": "http://purl.obolibrary.org/obo/PGDSO_", - "PLANA": "http://purl.obolibrary.org/obo/PLANA_", - "PLO": "http://purl.obolibrary.org/obo/PLO_", - "PO": "http://purl.obolibrary.org/obo/PO_", - "PORO": "http://purl.obolibrary.org/obo/PORO_", - "PPO": "http://purl.obolibrary.org/obo/PPO_", - "PR": "http://purl.obolibrary.org/obo/PR_", - "PROPREO": "http://purl.obolibrary.org/obo/PROPREO_", - "PW": "http://purl.obolibrary.org/obo/PW_", - "RESID": "http://purl.obolibrary.org/obo/RESID_", - "REX": "http://purl.obolibrary.org/obo/REX_", - "RNAO": "http://purl.obolibrary.org/obo/RNAO_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "RS": "http://purl.obolibrary.org/obo/RS_", - "RXNO": "http://purl.obolibrary.org/obo/RXNO_", - "SAO": "http://purl.obolibrary.org/obo/SAO_", - "SBO": "http://purl.obolibrary.org/obo/SBO_", - "SEP": "http://purl.obolibrary.org/obo/SEP_", - "SEPIO": "http://purl.obolibrary.org/obo/SEPIO_", - "SIBO": "http://purl.obolibrary.org/obo/SIBO_", - "SO": "http://purl.obolibrary.org/obo/SO_", - "SOPHARM": "http://purl.obolibrary.org/obo/SOPHARM_", - "SPD": "http://purl.obolibrary.org/obo/SPD_", - "STATO": "http://purl.obolibrary.org/obo/STATO_", - "SWO": "http://purl.obolibrary.org/obo/SWO_", - "SYMP": "http://purl.obolibrary.org/obo/SYMP_", - "TADS": "http://purl.obolibrary.org/obo/TADS_", - "TAHE": "http://purl.obolibrary.org/obo/TAHE_", - "TAHH": "http://purl.obolibrary.org/obo/TAHH_", - "TAO": "http://purl.obolibrary.org/obo/TAO_", - "TAXRANK": "http://purl.obolibrary.org/obo/TAXRANK_", - "TGMA": "http://purl.obolibrary.org/obo/TGMA_", - "TO": "http://purl.obolibrary.org/obo/TO_", - "TRANS": "http://purl.obolibrary.org/obo/TRANS_", - "TTO": "http://purl.obolibrary.org/obo/TTO_", - "UBERON": "http://purl.obolibrary.org/obo/UBERON_", - "UO": "http://purl.obolibrary.org/obo/UO_", - "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", - "VARIO": "http://purl.obolibrary.org/obo/VARIO_", - "VHOG": "http://purl.obolibrary.org/obo/VHOG_", - "VO": "http://purl.obolibrary.org/obo/VO_", - "VSAO": "http://purl.obolibrary.org/obo/VSAO_", - "VT": "http://purl.obolibrary.org/obo/VT_", - "VTO": "http://purl.obolibrary.org/obo/VTO_", - "WBBT": "http://purl.obolibrary.org/obo/WBBT_", - "WBLS": "http://purl.obolibrary.org/obo/WBLS_", - "WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_", - "XAO": "http://purl.obolibrary.org/obo/XAO_", - "XCO": "http://purl.obolibrary.org/obo/XCO_", - "XL": "http://purl.obolibrary.org/obo/XL_", - "YPO": "http://purl.obolibrary.org/obo/YPO_", - "ZEA": "http://purl.obolibrary.org/obo/ZEA_", - "ZECO": "http://purl.obolibrary.org/obo/ZECO_", - "ZFA": "http://purl.obolibrary.org/obo/ZFA_", - "ZFS": "http://purl.obolibrary.org/obo/ZFS_" - } -} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + OBOFoundry.github.io/context.jsonld at master · OBOFoundry/OBOFoundry.github.io · GitHub + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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{
"@context": {
"@base": "http://purl.obolibrary.org/obo/",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"owl": "http://www.w3.org/2002/07/owl#",
"xsd": "http://www.w3.org/2001/XMLSchema#",
"dc": "http://purl.org/dc/terms/",
"dce": "http://purl.org/dc/elements/1.1/",
"dct": "http://purl.org/dc/terms/1.1/",
"dcat":"http://www.w3.org/ns/dcat#",
"faldo": "http://biohackathon.org/resource/faldo#",
"foaf": "http://xmlns.com/foaf/0.1/",
"oa": "http://www.w3.org/ns/oa#",
"idot": "http://identifiers.org/",
"void": "http://rdfs.org/ns/void#",
"doap": "http://usefulinc.com/ns/doap#",
"pav": "http://purl.org/pav/",
"schemaorg": "http://schema.org/",
"disco": "http://rdf-vocabulary.ddialliance.org/discovery#",
+
"obofmd": "http://obofoundry.github.io/vocabulary/",
+
"obo": "http://purl.obolibrary.org/obo/",
"IAO": "obo:IAO_",
"NCBITaxon": "obo:NCBITaxon_",
"RO": "obo:RO_",
"BFO": "obo:BFO_",
+
"ontologies": "@graph",
"id": "@id",
"url": "@id",
"label": "rdfs:label",
"seeAlso": "rdfs:seeAlso",
"comment": "rdfs:comment",
"description": "dce:description",
"source": "dce:source",
"publisher": "dce:publisher",
"mailing_list": "doap:mailing-list",
"tracker": {
"@id": "doap:bug-database"
},
"funded_by": "disco:fundedBy",
"createdWith": "pav:createdWith",
"wasDerivedFrom": "pav:wasDerivedFrom",
"preferredPrefix": "idot:preferredPrefix",
"alternatePrefix": "idot:alternatePrefix",
"identifierPattern": "idot:identifierPattern",
"exampleIdentifier": "idot:exampleIdentifier",
"language": "dct:language",
"license": "dct:license",
"domain": "dct:theme",
"format": "dct:format",
"products": "dcat:distribution",
"Class": "owl:Class",
"biosharing": "rdfs:seeAlso",
"browsers": "rdfs:seeAlso",
+
"type": {
"@id": "rdf:type",
"@type": "@id"
},
"created": {
"@id": "dct:created",
"@type": "xsd:dateTime"
},
"creator": {
"@id": "dct:creator",
"@type": "@id"
},
"depiction": {
"@id": "foaf:depiction",
"@type": "@id"
},
"logo": {
"@id": "schemaorg:logo",
"@type": "@id"
},
"audience": {
"@id": "schemaorg:audience",
"@type": "schemaorg:Audience"
},
"contact": {
"@id": "dcat:contactPoint",
"@type": "foaf:Person"
},
"email": "foaf:mbox",
"build": {
"@id": "obofmd:has_build_information",
"@type": "obofmd:Build"
},
"checkout": "obofmd:checkout",
"method": "obofmd:method",
"source_url": {
"@id": "obofmd:source_url",
"@type": "xsd:anyURI"
},
"dependencies": "obofmd:depends_on",
"integration_server": "obofmd:continuous_integration_server",
"activity_status": "obofmd:activity_status",
+
"publications": "dct:publication",
"publisher": "dct:publisher",
"subClassOf": "owl:subClassOf",
"title": "dce:title",
"homepage": {
"@id": "foaf:homepage",
"@type": "@id"
},
"page": {
"@id": "foaf:page",
"@type": "@id"
},
"twitter": {
"@id": "foaf:account",
"@type": "@id"
},
"facebook": {
"@id": "foaf:account",
"@type": "@id"
},
"google_plus": {
"@id": "foaf:account",
"@type": "@id"
},
"is_about" : "IAO:0000136",
"taxon" : {
"@id": "IAO:0000136",
"@type": "owl:Class"
},
"ontology_purl": "dcat:accessURL",
"exampleClass": {
"@id": "void:exampleResource",
"@type": "@id"
}
}
}
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+ + + + + + + + + + + + + + + + + + + + + + From 91ee3009973a5b74d84618a85e61dba7478cb6e7 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 21 May 2021 08:37:01 -0700 Subject: [PATCH 3/5] update travis to use newer version of python --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 5a49db6..b25eef5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,6 @@ language: python python: - - "3.4" + - "3.7" # command to install dependencies install: From e29c4ba450723b3ed45bbfcaf6051a435605da3d Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 21 May 2021 08:41:13 -0700 Subject: [PATCH 4/5] update obo context --- registry/obo_context.jsonld | 2039 +++++------------------------------ 1 file changed, 248 insertions(+), 1791 deletions(-) diff --git a/registry/obo_context.jsonld b/registry/obo_context.jsonld index 5afcf51..d7667b8 100644 --- a/registry/obo_context.jsonld +++ b/registry/obo_context.jsonld @@ -1,1791 +1,248 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - OBOFoundry.github.io/context.jsonld at master · OBOFoundry/OBOFoundry.github.io · GitHub - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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{
"@context": {
"@base": "http://purl.obolibrary.org/obo/",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"owl": "http://www.w3.org/2002/07/owl#",
"xsd": "http://www.w3.org/2001/XMLSchema#",
"dc": "http://purl.org/dc/terms/",
"dce": "http://purl.org/dc/elements/1.1/",
"dct": "http://purl.org/dc/terms/1.1/",
"dcat":"http://www.w3.org/ns/dcat#",
"faldo": "http://biohackathon.org/resource/faldo#",
"foaf": "http://xmlns.com/foaf/0.1/",
"oa": "http://www.w3.org/ns/oa#",
"idot": "http://identifiers.org/",
"void": "http://rdfs.org/ns/void#",
"doap": "http://usefulinc.com/ns/doap#",
"pav": "http://purl.org/pav/",
"schemaorg": "http://schema.org/",
"disco": "http://rdf-vocabulary.ddialliance.org/discovery#",
-
"obofmd": "http://obofoundry.github.io/vocabulary/",
-
"obo": "http://purl.obolibrary.org/obo/",
"IAO": "obo:IAO_",
"NCBITaxon": "obo:NCBITaxon_",
"RO": "obo:RO_",
"BFO": "obo:BFO_",
-
"ontologies": "@graph",
"id": "@id",
"url": "@id",
"label": "rdfs:label",
"seeAlso": "rdfs:seeAlso",
"comment": "rdfs:comment",
"description": "dce:description",
"source": "dce:source",
"publisher": "dce:publisher",
"mailing_list": "doap:mailing-list",
"tracker": {
"@id": "doap:bug-database"
},
"funded_by": "disco:fundedBy",
"createdWith": "pav:createdWith",
"wasDerivedFrom": "pav:wasDerivedFrom",
"preferredPrefix": "idot:preferredPrefix",
"alternatePrefix": "idot:alternatePrefix",
"identifierPattern": "idot:identifierPattern",
"exampleIdentifier": "idot:exampleIdentifier",
"language": "dct:language",
"license": "dct:license",
"domain": "dct:theme",
"format": "dct:format",
"products": "dcat:distribution",
"Class": "owl:Class",
"biosharing": "rdfs:seeAlso",
"browsers": "rdfs:seeAlso",
-
"type": {
"@id": "rdf:type",
"@type": "@id"
},
"created": {
"@id": "dct:created",
"@type": "xsd:dateTime"
},
"creator": {
"@id": "dct:creator",
"@type": "@id"
},
"depiction": {
"@id": "foaf:depiction",
"@type": "@id"
},
"logo": {
"@id": "schemaorg:logo",
"@type": "@id"
},
"audience": {
"@id": "schemaorg:audience",
"@type": "schemaorg:Audience"
},
"contact": {
"@id": "dcat:contactPoint",
"@type": "foaf:Person"
},
"email": "foaf:mbox",
"build": {
"@id": "obofmd:has_build_information",
"@type": "obofmd:Build"
},
"checkout": "obofmd:checkout",
"method": "obofmd:method",
"source_url": {
"@id": "obofmd:source_url",
"@type": "xsd:anyURI"
},
"dependencies": "obofmd:depends_on",
"integration_server": "obofmd:continuous_integration_server",
"activity_status": "obofmd:activity_status",
-
"publications": "dct:publication",
"publisher": "dct:publisher",
"subClassOf": "owl:subClassOf",
"title": "dce:title",
"homepage": {
"@id": "foaf:homepage",
"@type": "@id"
},
"page": {
"@id": "foaf:page",
"@type": "@id"
},
"twitter": {
"@id": "foaf:account",
"@type": "@id"
},
"facebook": {
"@id": "foaf:account",
"@type": "@id"
},
"google_plus": {
"@id": "foaf:account",
"@type": "@id"
},
"is_about" : "IAO:0000136",
"taxon" : {
"@id": "IAO:0000136",
"@type": "owl:Class"
},
"ontology_purl": "dcat:accessURL",
"exampleClass": {
"@id": "void:exampleResource",
"@type": "@id"
}
}
}
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- - - - - - - - - - - - - - - - - - - - - - +{ + "@context": { + "AAO": "http://purl.obolibrary.org/obo/AAO_", + "ADW": "http://purl.obolibrary.org/obo/ADW_", + "AEO": "http://purl.obolibrary.org/obo/AEO_", + "AERO": "http://purl.obolibrary.org/obo/AERO_", + "AGRO": "http://purl.obolibrary.org/obo/AGRO_", + "AISM": "http://purl.obolibrary.org/obo/AISM_", + "AMPHX": "http://purl.obolibrary.org/obo/AMPHX_", + "APO": "http://purl.obolibrary.org/obo/APO_", + "APOLLO_SV": "http://purl.obolibrary.org/obo/APOLLO_SV_", + "ARO": "http://purl.obolibrary.org/obo/ARO_", + "ATO": "http://purl.obolibrary.org/obo/ATO_", + "BCGO": "http://purl.obolibrary.org/obo/BCGO_", + "BCO": "http://purl.obolibrary.org/obo/BCO_", + "BFO": "http://purl.obolibrary.org/obo/BFO_", + "BILA": "http://purl.obolibrary.org/obo/BILA_", + "BOOTSTREP": "http://purl.obolibrary.org/obo/BOOTSTREP_", + "BSPO": "http://purl.obolibrary.org/obo/BSPO_", + "BTO": "http://purl.obolibrary.org/obo/BTO_", + "CARO": "http://purl.obolibrary.org/obo/CARO_", + "CDAO": "http://purl.obolibrary.org/obo/CDAO_", + "CDNO": "http://purl.obolibrary.org/obo/CDNO_", + "CEPH": "http://purl.obolibrary.org/obo/CEPH_", + "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", + "CHEMINF": "http://purl.obolibrary.org/obo/CHEMINF_", + "CHIRO": "http://purl.obolibrary.org/obo/CHIRO_", + "CHMO": "http://purl.obolibrary.org/obo/CHMO_", + "CIDO": "http://purl.obolibrary.org/obo/CIDO_", + "CIO": "http://purl.obolibrary.org/obo/CIO_", + "CL": "http://purl.obolibrary.org/obo/CL_", + "CLAO": "http://purl.obolibrary.org/obo/CLAO_", + "CLO": "http://purl.obolibrary.org/obo/CLO_", + "CLYH": "http://purl.obolibrary.org/obo/CLYH_", + "CMF": "http://purl.obolibrary.org/obo/CMF_", + "CMO": "http://purl.obolibrary.org/obo/CMO_", + "COB": "http://purl.obolibrary.org/obo/COB_", + "CRO": "http://purl.obolibrary.org/obo/CRO_", + "CTENO": "http://purl.obolibrary.org/obo/CTENO_", + "CTO": "http://purl.obolibrary.org/obo/CTO_", + "CVDO": "http://purl.obolibrary.org/obo/CVDO_", + "DC_CL": "http://purl.obolibrary.org/obo/DC_CL_", + "DDANAT": "http://purl.obolibrary.org/obo/DDANAT_", + "DDPHENO": "http://purl.obolibrary.org/obo/DDPHENO_", + "DIDEO": "http://purl.obolibrary.org/obo/DIDEO_", + "DINTO": "http://purl.obolibrary.org/obo/DINTO_", + "DOID": "http://purl.obolibrary.org/obo/DOID_", + "DRON": "http://purl.obolibrary.org/obo/DRON_", + "DUO": "http://purl.obolibrary.org/obo/DUO_", + "ECAO": "http://purl.obolibrary.org/obo/ECAO_", + "ECO": "http://purl.obolibrary.org/obo/ECO_", + "ECOCORE": "http://purl.obolibrary.org/obo/ECOCORE_", + "ECTO": "http://purl.obolibrary.org/obo/ECTO_", + "EHDA": "http://purl.obolibrary.org/obo/EHDA_", + "EHDAA": "http://purl.obolibrary.org/obo/EHDAA_", + "EHDAA2": "http://purl.obolibrary.org/obo/EHDAA2_", + "EMAP": "http://purl.obolibrary.org/obo/EMAP_", + "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", + "ENVO": "http://purl.obolibrary.org/obo/ENVO_", + "EO": "http://purl.obolibrary.org/obo/EO_", + "EPO": "http://purl.obolibrary.org/obo/EPO_", + "ERO": "http://purl.obolibrary.org/obo/ERO_", + "EUPATH": "http://purl.obolibrary.org/obo/EUPATH_", + "EV": "http://purl.obolibrary.org/obo/EV_", + "ExO": "http://purl.obolibrary.org/obo/ExO_", + "FAO": "http://purl.obolibrary.org/obo/FAO_", + "FBSP": "http://purl.obolibrary.org/obo/FBSP_", + "FBbi": "http://purl.obolibrary.org/obo/FBbi_", + "FBbt": "http://purl.obolibrary.org/obo/FBbt_", + "FBcv": "http://purl.obolibrary.org/obo/FBcv_", + "FBdv": "http://purl.obolibrary.org/obo/FBdv_", + "FIDEO": "http://purl.obolibrary.org/obo/FIDEO_", + "FIX": "http://purl.obolibrary.org/obo/FIX_", + "FLOPO": "http://purl.obolibrary.org/obo/FLOPO_", + "FLU": "http://purl.obolibrary.org/obo/FLU_", + "FMA": "http://purl.obolibrary.org/obo/FMA_", + "FOBI": "http://purl.obolibrary.org/obo/FOBI_", + "FOODON": "http://purl.obolibrary.org/obo/FOODON_", + "FOVT": "http://purl.obolibrary.org/obo/FOVT_", + "FYPO": "http://purl.obolibrary.org/obo/FYPO_", + "GAZ": "http://purl.obolibrary.org/obo/GAZ_", + "GECKO": "http://purl.obolibrary.org/obo/GECKO_", + "GENEPIO": "http://purl.obolibrary.org/obo/GENEPIO_", + "GENO": "http://purl.obolibrary.org/obo/GENO_", + "GEO": "http://purl.obolibrary.org/obo/GEO_", + "GNO": "http://purl.obolibrary.org/obo/GNO_", + "GO": "http://purl.obolibrary.org/obo/GO_", + "GRO": "http://purl.obolibrary.org/obo/GRO_", + "GSSO": "http://purl.obolibrary.org/obo/GSSO_", + "HABRONATTUS": "http://purl.obolibrary.org/obo/HABRONATTUS_", + "HANCESTRO": "http://purl.obolibrary.org/obo/HANCESTRO_", + "HAO": "http://purl.obolibrary.org/obo/HAO_", + "HOM": "http://purl.obolibrary.org/obo/HOM_", + "HP": "http://purl.obolibrary.org/obo/HP_", + "HSO": "http://purl.obolibrary.org/obo/HSO_", + "HTN": "http://purl.obolibrary.org/obo/HTN_", + "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_", + "IAO": "http://purl.obolibrary.org/obo/IAO_", + "ICEO": "http://purl.obolibrary.org/obo/ICEO_", + "ICO": "http://purl.obolibrary.org/obo/ICO_", + "IDO": "http://purl.obolibrary.org/obo/IDO_", + "IDOMAL": "http://purl.obolibrary.org/obo/IDOMAL_", + "IEV": "http://purl.obolibrary.org/obo/IEV_", + "IMR": "http://purl.obolibrary.org/obo/IMR_", + "INO": "http://purl.obolibrary.org/obo/INO_", + "IPR": "http://purl.obolibrary.org/obo/IPR_", + "KISAO": "http://purl.obolibrary.org/obo/KISAO_", + "LABO": "http://purl.obolibrary.org/obo/LABO_", + "LIPRO": "http://purl.obolibrary.org/obo/LIPRO_", + "LOGGERHEAD": "http://purl.obolibrary.org/obo/LOGGERHEAD_", + "MA": "http://purl.obolibrary.org/obo/MA_", + "MAMO": "http://purl.obolibrary.org/obo/MAMO_", + "MAO": "http://purl.obolibrary.org/obo/MAO_", + "MAT": "http://purl.obolibrary.org/obo/MAT_", + "MAXO": "http://purl.obolibrary.org/obo/MAXO_", + "MCO": "http://purl.obolibrary.org/obo/MCO_", + "MF": "http://purl.obolibrary.org/obo/MF_", + "MFMO": "http://purl.obolibrary.org/obo/MFMO_", + "MFO": "http://purl.obolibrary.org/obo/MFO_", + "MFOEM": "http://purl.obolibrary.org/obo/MFOEM_", + "MFOMD": "http://purl.obolibrary.org/obo/MFOMD_", + "MI": "http://purl.obolibrary.org/obo/MI_", + "MIAPA": "http://purl.obolibrary.org/obo/MIAPA_", + "MICRO": "http://purl.obolibrary.org/obo/MICRO_", + "MIRNAO": "http://purl.obolibrary.org/obo/MIRNAO_", + "MIRO": "http://purl.obolibrary.org/obo/MIRO_", + "MMO": "http://purl.obolibrary.org/obo/MMO_", + "MO": "http://purl.obolibrary.org/obo/MO_", + "MOD": "http://purl.obolibrary.org/obo/MOD_", + "MONDO": "http://purl.obolibrary.org/obo/MONDO_", + "MOP": "http://purl.obolibrary.org/obo/MOP_", + "MP": "http://purl.obolibrary.org/obo/MP_", + "MPATH": "http://purl.obolibrary.org/obo/MPATH_", + "MPIO": "http://purl.obolibrary.org/obo/MPIO_", + "MRO": "http://purl.obolibrary.org/obo/MRO_", + "MS": "http://purl.obolibrary.org/obo/MS_", + "MmusDv": "http://purl.obolibrary.org/obo/MmusDv_", + "NBO": "http://purl.obolibrary.org/obo/NBO_", + "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", + "NCIT": "http://purl.obolibrary.org/obo/NCIT_", + "NCRO": "http://purl.obolibrary.org/obo/NCRO_", + "NIF_CELL": "http://purl.obolibrary.org/obo/NIF_CELL_", + "NIF_DYSFUNCTION": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_", + "NIF_GROSSANATOMY": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_", + "NMR": "http://purl.obolibrary.org/obo/NMR_", + "NOMEN": "http://purl.obolibrary.org/obo/NOMEN_", + "OAE": "http://purl.obolibrary.org/obo/OAE_", + "OARCS": "http://purl.obolibrary.org/obo/OARCS_", + "OBA": "http://purl.obolibrary.org/obo/OBA_", + "OBCS": "http://purl.obolibrary.org/obo/OBCS_", + "OBI": "http://purl.obolibrary.org/obo/OBI_", + "OBIB": "http://purl.obolibrary.org/obo/OBIB_", + "OBO_REL": "http://purl.obolibrary.org/obo/OBO_REL_", + "OGG": "http://purl.obolibrary.org/obo/OGG_", + "OGI": "http://purl.obolibrary.org/obo/OGI_", + "OGMS": "http://purl.obolibrary.org/obo/OGMS_", + "OGSF": "http://purl.obolibrary.org/obo/OGSF_", + "OHD": "http://purl.obolibrary.org/obo/OHD_", + "OHMI": "http://purl.obolibrary.org/obo/OHMI_", + "OHPI": "http://purl.obolibrary.org/obo/OHPI_", + "OMIABIS": "http://purl.obolibrary.org/obo/OMIABIS_", + "OMIT": "http://purl.obolibrary.org/obo/OMIT_", + "OMO": "http://purl.obolibrary.org/obo/OMO_", + "OMP": "http://purl.obolibrary.org/obo/OMP_", + "OMRSE": "http://purl.obolibrary.org/obo/OMRSE_", + "ONE": "http://purl.obolibrary.org/obo/ONE_", + "ONS": "http://purl.obolibrary.org/obo/ONS_", + "ONTONEO": "http://purl.obolibrary.org/obo/ONTONEO_", + "OOSTT": "http://purl.obolibrary.org/obo/OOSTT_", + "OPL": "http://purl.obolibrary.org/obo/OPL_", + "OPMI": "http://purl.obolibrary.org/obo/OPMI_", + "ORNASEQ": "http://purl.obolibrary.org/obo/ORNASEQ_", + "OVAE": "http://purl.obolibrary.org/obo/OVAE_", + "OlatDv": "http://purl.obolibrary.org/obo/OlatDv_", + "PAO": "http://purl.obolibrary.org/obo/PAO_", + "PATO": "http://purl.obolibrary.org/obo/PATO_", + "PCO": "http://purl.obolibrary.org/obo/PCO_", + "PDRO": "http://purl.obolibrary.org/obo/PDRO_", + "PD_ST": "http://purl.obolibrary.org/obo/PD_ST_", + "PECO": "http://purl.obolibrary.org/obo/PECO_", + "PGDSO": "http://purl.obolibrary.org/obo/PGDSO_", + "PHIPO": "http://purl.obolibrary.org/obo/PHIPO_", + "PLANA": "http://purl.obolibrary.org/obo/PLANA_", + "PLANP": "http://purl.obolibrary.org/obo/PLANP_", + "PLO": "http://purl.obolibrary.org/obo/PLO_", + "PO": "http://purl.obolibrary.org/obo/PO_", + "PORO": "http://purl.obolibrary.org/obo/PORO_", + "PPO": "http://purl.obolibrary.org/obo/PPO_", + "PR": "http://purl.obolibrary.org/obo/PR_", + "PROPREO": "http://purl.obolibrary.org/obo/PROPREO_", + "PSDO": "http://purl.obolibrary.org/obo/PSDO_", + "PSO": "http://purl.obolibrary.org/obo/PSO_", + "PW": "http://purl.obolibrary.org/obo/PW_", + "PdumDv": "http://purl.obolibrary.org/obo/PdumDv_", + "RBO": "http://purl.obolibrary.org/obo/RBO_", + "RESID": "http://purl.obolibrary.org/obo/RESID_", + "REX": "http://purl.obolibrary.org/obo/REX_", + "RNAO": "http://purl.obolibrary.org/obo/RNAO_", + "RO": "http://purl.obolibrary.org/obo/RO_", + "RS": "http://purl.obolibrary.org/obo/RS_", + "RXNO": "http://purl.obolibrary.org/obo/RXNO_", + "SAO": "http://purl.obolibrary.org/obo/SAO_", + "SBO": "http://purl.obolibrary.org/obo/SBO_", + "SCDO": "http://purl.obolibrary.org/obo/SCDO_", + "SEP": "http://purl.obolibrary.org/obo/SEP_", + "SEPIO": "http://purl.obolibrary.org/obo/SEPIO_", + "SIBO": "http://purl.obolibrary.org/obo/SIBO_", + "SO": "http://purl.obolibrary.org/obo/SO_", + "SOPHARM": "http://purl.obolibrary.org/obo/SOPHARM_", + "SPD": "http://purl.obolibrary.org/obo/SPD_", + "STATO": "http://purl.obolibrary.org/obo/STATO_", + "SWO": "http://purl.obolibrary.org/obo/SWO_", + "SYMP": "http://purl.obolibrary.org/obo/SYMP_", + "TADS": "http://purl.obolibrary.org/obo/TADS_", + "TAHE": "http://purl.obolibrary.org/obo/TAHE_", + "TAHH": "http://purl.obolibrary.org/obo/TAHH_", + "TAO": "http://purl.obolibrary.org/obo/TAO_", + "TAXRANK": "http://purl.obolibrary.org/obo/TAXRANK_", + "TGMA": "http://purl.obolibrary.org/obo/TGMA_", + "TO": "http://purl.obolibrary.org/obo/TO_", + "TRANS": "http://purl.obolibrary.org/obo/TRANS_", + "TTO": "http://purl.obolibrary.org/obo/TTO_", + "TXPO": "http://purl.obolibrary.org/obo/TXPO_", + "UBERON": "http://purl.obolibrary.org/obo/UBERON_", + "UO": "http://purl.obolibrary.org/obo/UO_", + "UPA": "http://purl.obolibrary.org/obo/UPA_", + "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", + "VARIO": "http://purl.obolibrary.org/obo/VARIO_", + "VHOG": "http://purl.obolibrary.org/obo/VHOG_", + "VO": "http://purl.obolibrary.org/obo/VO_", + "VSAO": "http://purl.obolibrary.org/obo/VSAO_", + "VT": "http://purl.obolibrary.org/obo/VT_", + "VTO": "http://purl.obolibrary.org/obo/VTO_", + "WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_", + "WBbt": "http://purl.obolibrary.org/obo/WBbt_", + "WBls": "http://purl.obolibrary.org/obo/WBls_", + "XAO": "http://purl.obolibrary.org/obo/XAO_", + "XCO": "http://purl.obolibrary.org/obo/XCO_", + "XLMOD": "http://purl.obolibrary.org/obo/XLMOD_", + "XPO": "http://purl.obolibrary.org/obo/XPO_", + "YPO": "http://purl.obolibrary.org/obo/YPO_", + "ZEA": "http://purl.obolibrary.org/obo/ZEA_", + "ZECO": "http://purl.obolibrary.org/obo/ZECO_", + "ZFA": "http://purl.obolibrary.org/obo/ZFA_", + "ZFS": "http://purl.obolibrary.org/obo/ZFS_", + "ZP": "http://purl.obolibrary.org/obo/ZP_" + } +} From a51ec76aab1cdffbc8378a36b26ec1cdd4f2715d Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 21 May 2021 09:18:03 -0700 Subject: [PATCH 5/5] get makefile working --- Makefile | 12 +-- registry/commons_context.jsonld | 132 ++++++++++++++++++++++++-------- registry/idot_nr_context.jsonld | 2 +- registry/monarch_context.jsonld | 79 ++++++++++++------- reports/clashes.txt | 29 +++---- 5 files changed, 175 insertions(+), 79 deletions(-) diff --git a/Makefile b/Makefile index 100fb8d..8d5a30b 100644 --- a/Makefile +++ b/Makefile @@ -28,8 +28,8 @@ registry/obo_context.jsonld: trigger registry/minerva_context.jsonld: trigger wget --no-check-certificate https://raw.githubusercontent.com/geneontology/minerva/master/minerva-core/src/main/resources/amigo_context_manual.jsonld -O $@ && touch $@ -registry/go_context.jsonld: registry/go-db-xrefs.json - ./bin/go-xrefs-to-context.py $< > $@.tmp && mv $@.tmp $@ +#registry/go_context.jsonld: registry/go-db-xrefs.json +# ./bin/go-xrefs-to-context.py $< > $@.tmp && mv $@.tmp $@ ## Monarch registry/monarch_curie_map.yaml: @@ -45,13 +45,13 @@ registry/pr_context.jsonld: ## IDENTIFIERS.ORG ## Step1: Get miriam -registry/miriam.ttl: trigger - wget --no-check-certificate http://www.ebi.ac.uk/miriam/main/export/registry.ttl -O $@ && touch $@ +#registry/miriam.ttl: trigger +# wget --no-check-certificate http://www.ebi.ac.uk/miriam/main/export/registry.ttl -O $@ && touch $@ ## ## Everything from MIRIAM registry -registry/idot_context.jsonld: registry/miriam.ttl - ./bin/miriam2jsonld.pl $< > $@ +#registry/idot_context.jsonld: registry/miriam.ttl +# ./bin/miriam2jsonld.pl $< > $@ ## NON-REDUNDANT IDOT ## diff --git a/registry/commons_context.jsonld b/registry/commons_context.jsonld index 7c60f16..faf6b1d 100644 --- a/registry/commons_context.jsonld +++ b/registry/commons_context.jsonld @@ -1,6 +1,6 @@ { "@context": { - "dc": "http://purl.org/dc/elements/1.1/", + "dc": "http://purl.org/dc/terms/", "dcat": "http://www.w3.org/ns/dcat#", "dcterms": "http://purl.org/dc/terms/", "faldo": "http://biohackathon.org/resource/faldo#", @@ -106,7 +106,7 @@ "GENECARDS": "http://identifiers.org/genecards/", "MICROSCOPE": "http://identifiers.org/microscope/", "SWISSREGULON": "http://identifiers.org/swissregulon/", - "EFO": "http://purl.obolibrary.org/obo/EFO_", + "EFO": "http://www.ebi.ac.uk/efo/EFO_", "CYGD": "http://identifiers.org/cygd/", "METLIN": "http://identifiers.org/metlin/", "UMBBD.ENZYME": "http://identifiers.org/umbbd.enzyme/", @@ -128,7 +128,7 @@ "DATF": "http://identifiers.org/datf/", "DBD": "http://identifiers.org/dbd/", "TREEFAM": "http://identifiers.org/treefam/", - "MESH": "http://purl.obolibrary.org/obo/MESH_", + "MESH": "http://id.nlm.nih.gov/mesh/", "ARDB": "http://identifiers.org/ardb/", "MIRIAM.COLLECTION": "http://identifiers.org/miriam.collection/", "LGIC": "http://identifiers.org/lgic/", @@ -183,7 +183,7 @@ "VBASE2": "http://identifiers.org/vbase2/", "BIND": "http://identifiers.org/bind/", "FBOL": "http://identifiers.org/fbol/", - "HGNC": "http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=", + "HGNC": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:", "FAIRSHARING": "http://identifiers.org/fairsharing/", "MIRBASE.MATURE": "http://identifiers.org/mirbase.mature/", "DBSNP": "http://identifiers.org/dbsnp/", @@ -469,7 +469,7 @@ "NONCODEV4.GENE": "http://identifiers.org/noncodev4.gene/", "WIKIGENES": "http://identifiers.org/wikigenes/", "GWASCENTRAL.STUDY": "http://identifiers.org/gwascentral.study/", - "NCBIGENE": "http://identifiers.org/ncbigene/", + "NCBIGene": "https://www.ncbi.nlm.nih.gov/gene/", "GRID": "http://identifiers.org/grid/", "SIDER.EFFECT": "http://identifiers.org/sider.effect/", "EXAC.VARIANT": "http://identifiers.org/exac.variant/", @@ -633,7 +633,7 @@ "MEROPS.INHIBITOR": "http://identifiers.org/merops.inhibitor/", "GMD.GCMS": "http://identifiers.org/gmd.gcms/", "NEUROVAULT.IMAGE": "http://identifiers.org/neurovault.image/", - "OMIA": "http://purl.obolibrary.org/obo/OMIA_", + "OMIA": "https://omia.org/OMIA", "CHEMBANK": "http://identifiers.org/chembank/", "BIOCATALOGUE.SERVICE": "http://identifiers.org/biocatalogue.service/", "FB": "http://identifiers.org/fb/", @@ -655,9 +655,13 @@ "APO": "http://purl.obolibrary.org/obo/APO_", "AQTLPub": "https://www.animalgenome.org/cgi-bin/QTLdb/BT/qabstract?PUBMED_ID=", "AQTLTrait": "http://identifiers.org/animalqtltrait/", + "AspGD": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=", + "AspGD_REF": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=", "BFO": "http://purl.obolibrary.org/obo/BFO_", + "BGD": "http://bovinegenome.org/genepages/btau40/genes/", "BNODE": "https://monarchinitiative.org/.well-known/genid/", "BT": "http://c.biothings.io/#", + "CGNC": "http://birdgenenames.org/cgnc/GeneReport?id=", "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", "CHR": "http://purl.obolibrary.org/obo/CHR_", "CID": "http://pubchem.ncbi.nlm.nih.gov/compound/", @@ -665,52 +669,64 @@ "CLO": "http://purl.obolibrary.org/obo/CLO_", "CMMR": "http://www.cmmr.ca/order.php?t=m&id=", "CMO": "http://purl.obolibrary.org/obo/CMO_", + "COHD": "http://purl.obolibrary.org/obo/COHD_", "ClinVar": "http://www.ncbi.nlm.nih.gov/clinvar/", "ClinVarSubmitters": "http://www.ncbi.nlm.nih.gov/clinvar/submitters/", "ClinVarVariant": "http://www.ncbi.nlm.nih.gov/clinvar/variation/", + "ComplexPortal": "https://www.ebi.ac.uk/complexportal/complex/", "Coriell": "https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=", "CoriellCollection": "https://catalog.coriell.org/1/", "CoriellFamily": "https://catalog.coriell.org/0/Sections/BrowseCatalog/FamilyTypeSubDetail.aspx?fam=", "CoriellIndividual": "https://catalog.coriell.org/Search?q=", - "DATA": "http://edamontology.org/data_", "DC_CL": "http://purl.obolibrary.org/obo/DC_CL_", - "DECIPHER": "http://purl.obolibrary.org/obo/DECIPHER_", + "DECIPHER": "https://decipher.sanger.ac.uk/syndrome/", "DOID": "http://purl.obolibrary.org/obo/DOID_", "DrugBank": "http://www.drugbank.ca/drugs/", - "EC": "http://www.enzyme-database.org/query.php?ec=", + "EC": "https://www.enzyme-database.org/query.php?ec=", "ECO": "http://purl.obolibrary.org/obo/ECO_", + "EDAM-DATA": "http://edamontology.org/data_", "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", "EMMA": "https://www.infrafrontier.eu/search?keyword=EM:", "ENVO": "http://purl.obolibrary.org/obo/ENVO_", - "EOM": "http://purl.obolibrary.org/obo/EOM_", + "EOM": "https://elementsofmorphology.nih.gov/index.cgi?tid=", + "EOM_IMG": "https://elementsofmorphology.nih.gov/images/terms/", "ERO": "http://purl.obolibrary.org/obo/ERO_", "EcoGene": "http://ecogene.org/gene/", + "EnsemblGenome": "http://www.ensemblgenomes.org/id/", "FBbt": "http://purl.obolibrary.org/obo/FBbt_", "FBcv": "http://purl.obolibrary.org/obo/FBcv_", "FBdv": "http://purl.obolibrary.org/obo/FBdv_", "FDADrug": "http://www.fda.gov/Drugs/InformationOnDrugs/", "FlyBase": "http://flybase.org/reports/", + "GARD": "http://purl.obolibrary.org/obo/GARD_", "GENO": "http://purl.obolibrary.org/obo/GENO_", "GINAS": "http://tripod.nih.gov/ginas/app/substance#", "GO": "http://purl.obolibrary.org/obo/GO_", "GO_REF": "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:", + "GWAS": "https://www.ebi.ac.uk/gwas/variants/", "GenBank": "http://www.ncbi.nlm.nih.gov/nuccore/", + "Genatlas": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=", "GeneReviews": "http://www.ncbi.nlm.nih.gov/books/", "HP": "http://purl.obolibrary.org/obo/HP_", "HPO": "http://human-phenotype-ontology.org/", "IAO": "http://purl.obolibrary.org/obo/IAO_", - "IMPC": "http://www.mousephenotype.org/data/genes/", - "IMPRESS-parameter": "https://www.mousephenotype.org/impress/parameterontologies/", - "IMPRESS-procedure": "https://www.mousephenotype.org/impress/procedures/", - "IMPRESS-protocol": "https://www.mousephenotype.org/impress/protocol/", + "ICD9": "http://purl.obolibrary.org/obo/ICD9_", + "IMPC": "https://www.mousephenotype.org/data/genes/", + "IMPC-param": "https://www.mousephenotype.org/impress/OntologyInfo?action=list&procID=", + "IMPC-pipe": "https://www.mousephenotype.org/impress/PipelineInfo?id=", + "IMPC-proc": "https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=", "ISBN-10": "https://monarchinitiative.org/ISBN10_", "ISBN-13": "https://monarchinitiative.org/ISBN13_", + "IUPHAR": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=", + "InterPro": "https://www.ebi.ac.uk/interpro/entry/InterPro/", "J": "http://www.informatics.jax.org/reference/J:", "JAX": "http://jaxmice.jax.org/strain/", "KEGG-ds": "http://purl.obolibrary.org/KEGG-ds_", "KEGG-hsa": "http://www.kegg.jp/dbget-bin/www_bget?hsa:", + "KEGG-img": "http://www.genome.jp/kegg/pathway/map/", "KEGG-ko": "http://www.kegg.jp/dbget-bin/www_bget?ko:", "KEGG-path": "http://www.kegg.jp/dbget-bin/www_bget?path:", + "LIDA": "http://sydney.edu.au/vetscience/lida/dogs/search/disorder/", "LPT": "http://purl.obolibrary.org/obo/LPT_", "MA": "http://purl.obolibrary.org/obo/MA_", "MONARCH": "https://monarchinitiative.org/MONARCH_", @@ -722,12 +738,13 @@ "MPD-strain": "http://phenome.jax.org/db/q?rtn=strains/details&strainid=", "MUGEN": "http://bioit.fleming.gr/mugen/Controller?workflow=ViewModel&expand_all=true&name_begins=model.block&eid=", "MedGen": "http://www.ncbi.nlm.nih.gov/medgen/", - "MonarchArchive": "https://archive.monarchinitiative.org/201806/", + "MonarchArchive": "https://archive.monarchinitiative.org/", "MonarchData": "https://data.monarchinitiative.org/ttl/", + "MonarchLogoRepo": "https://github.com/monarch-initiative/monarch-ui/blob/master/public/img/sources/", "NBO": "http://purl.obolibrary.org/obo/NBO_", - "NCBIAssembly": "http://www.ncbi.nlm.nih.gov/assembly/", - "NCBIGene": "http://www.ncbi.nlm.nih.gov/gene/", - "NCBIGenome": "http://www.ncbi.nlm.nih.gov/genome/", + "NCBIAssembly": "https://www.ncbi.nlm.nih.gov/assembly?term=", + "NCBIBSgene": "http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=", + "NCBIGenome": "https://www.ncbi.nlm.nih.gov/genome/", "NCBIProtein": "http://www.ncbi.nlm.nih.gov/protein/", "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", "NCIMR": "https://mouse.ncifcrf.gov/available_details.asp?ID=", @@ -737,10 +754,10 @@ "OBAN": "http://purl.org/oban/", "OBI": "http://purl.obolibrary.org/obo/OBI_", "OBO": "http://purl.obolibrary.org/obo/", - "OIO": "http://www.geneontology.org/formats/oboInOwl#", "OMIA-breed": "https://monarchinitiative.org/model/OMIA-breed:", - "OMIM": "http://purl.obolibrary.org/obo/OMIM_", - "Orphanet": "http://www.orpha.net/ORDO/Orphanet_", + "OMIM": "http://omim.org/entry/", + "OMIMPS": "http://www.omim.org/phenotypicSeries/", + "ORPHA": "http://www.orpha.net/ORDO/Orphanet_", "PAINT_REF": "http://www.geneontology.org/gene-associations/submission/paint/", "PANTHER": "http://www.pantherdb.org/panther/family.do?clsAccession=", "PATO": "http://purl.obolibrary.org/obo/PATO_", @@ -750,12 +767,13 @@ "PR": "http://purl.obolibrary.org/obo/PR_", "PW": "http://purl.obolibrary.org/obo/PW_", "PomBase": "https://www.pombase.org/spombe/result/", - "RBRC": "http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=RBRC", + "RBRC": "http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=", "REACT": "http://www.reactome.org/PathwayBrowser/#/", "RGDRef": "http://rgd.mcw.edu/rgdweb/report/reference/main.html?id=", "RO": "http://purl.obolibrary.org/obo/RO_", "RXCUI": "http://purl.bioontology.org/ontology/RXNORM/", "RefSeq": "http://www.ncbi.nlm.nih.gov/refseq/?term=", + "SCTID": "http://purl.obolibrary.org/obo/SCTID_", "SEPIO": "http://purl.obolibrary.org/obo/SEPIO_", "SGD_REF": "https://www.yeastgenome.org/reference/", "SIO": "http://semanticscience.org/resource/SIO_", @@ -767,9 +785,11 @@ "TrEMBL": "http://purl.uniprot.org/uniprot/", "UBERON": "http://purl.obolibrary.org/obo/UBERON_", "UCSC": "ftp://hgdownload.cse.ucsc.edu/goldenPath/", + "UCSCBuild": "http://genome.ucsc.edu/cgi-bin/hgGateway?db=", "UO": "http://purl.obolibrary.org/obo/UO_", "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", "UniProtKB": "http://identifiers.org/uniprot/", + "VGNC": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/", "VIVO": "http://vivoweb.org/ontology/core#", "VT": "http://purl.obolibrary.org/obo/VT_", "WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_", @@ -779,30 +799,39 @@ "WormBase": "https://www.wormbase.org/get?name=", "XAO": "http://purl.obolibrary.org/obo/XAO_", "XCO": "http://purl.obolibrary.org/obo/XCO_", - "Xenbase": "http://www.xenbase.org/gene/showgene.do?method=display&geneId=", + "XPO": "http://purl.obolibrary.org/obo/XPO_", + "Xenbase": "http://identifiers.org/xenbase/", "ZFA": "http://purl.obolibrary.org/obo/ZFA_", "ZFS": "http://purl.obolibrary.org/obo/ZFS_", "ZP": "http://purl.obolibrary.org/obo/ZP_", + "biolink": "https://w3id.org/biolink/vocab/", "catfishQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/IP/qdetails?QTL_ID=", - "cattleQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_D=", + "cattleQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=", "chickenQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=", + "cito": "http://purl.org/spar/cito/", "dbSNP": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=", "dbSNPIndividual": "http://www.ncbi.nlm.nih.gov/SNP/snp_ind.cgi?ind_id=", "dbVar": "http://www.ncbi.nlm.nih.gov/dbvar/", "dctypes": "http://purl.org/dc/dcmitype/", "dictyBase": "http://dictybase.org/gene/", "horseQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/EC/qdetails?QTL_ID=", + "miRBase": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=", "pav": "http://purl.org/pav/", "pigQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=", "rainbow_troutQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/OM/qdetails?QTL_ID=", + "schema": "http://schema.org/", "sheepQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=", - "skos": "https://www.w3.org/TR/skos-reference/#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "vfb": "http://virtualflybrain.org/reports/", "xml": "http://www.w3.org/XML/1998/namespace", "AAO": "http://purl.obolibrary.org/obo/AAO_", "ADW": "http://purl.obolibrary.org/obo/ADW_", "AEO": "http://purl.obolibrary.org/obo/AEO_", "AERO": "http://purl.obolibrary.org/obo/AERO_", "AGRO": "http://purl.obolibrary.org/obo/AGRO_", + "AISM": "http://purl.obolibrary.org/obo/AISM_", + "AMPHX": "http://purl.obolibrary.org/obo/AMPHX_", + "APOLLO_SV": "http://purl.obolibrary.org/obo/APOLLO_SV_", "ARO": "http://purl.obolibrary.org/obo/ARO_", "ATO": "http://purl.obolibrary.org/obo/ATO_", "BCGO": "http://purl.obolibrary.org/obo/BCGO_", @@ -813,13 +842,20 @@ "BTO": "http://purl.obolibrary.org/obo/BTO_", "CARO": "http://purl.obolibrary.org/obo/CARO_", "CDAO": "http://purl.obolibrary.org/obo/CDAO_", + "CDNO": "http://purl.obolibrary.org/obo/CDNO_", "CEPH": "http://purl.obolibrary.org/obo/CEPH_", "CHEMINF": "http://purl.obolibrary.org/obo/CHEMINF_", + "CHIRO": "http://purl.obolibrary.org/obo/CHIRO_", "CHMO": "http://purl.obolibrary.org/obo/CHMO_", + "CIDO": "http://purl.obolibrary.org/obo/CIDO_", "CIO": "http://purl.obolibrary.org/obo/CIO_", + "CLAO": "http://purl.obolibrary.org/obo/CLAO_", + "CLYH": "http://purl.obolibrary.org/obo/CLYH_", "CMF": "http://purl.obolibrary.org/obo/CMF_", + "COB": "http://purl.obolibrary.org/obo/COB_", "CRO": "http://purl.obolibrary.org/obo/CRO_", "CTENO": "http://purl.obolibrary.org/obo/CTENO_", + "CTO": "http://purl.obolibrary.org/obo/CTO_", "CVDO": "http://purl.obolibrary.org/obo/CVDO_", "DDANAT": "http://purl.obolibrary.org/obo/DDANAT_", "DDPHENO": "http://purl.obolibrary.org/obo/DDPHENO_", @@ -827,7 +863,9 @@ "DINTO": "http://purl.obolibrary.org/obo/DINTO_", "DRON": "http://purl.obolibrary.org/obo/DRON_", "DUO": "http://purl.obolibrary.org/obo/DUO_", + "ECAO": "http://purl.obolibrary.org/obo/ECAO_", "ECOCORE": "http://purl.obolibrary.org/obo/ECOCORE_", + "ECTO": "http://purl.obolibrary.org/obo/ECTO_", "EHDA": "http://purl.obolibrary.org/obo/EHDA_", "EHDAA": "http://purl.obolibrary.org/obo/EHDAA_", "EHDAA2": "http://purl.obolibrary.org/obo/EHDAA2_", @@ -836,36 +874,50 @@ "EPO": "http://purl.obolibrary.org/obo/EPO_", "EUPATH": "http://purl.obolibrary.org/obo/EUPATH_", "EV": "http://purl.obolibrary.org/obo/EV_", - "EXO": "http://purl.obolibrary.org/obo/EXO_", + "ExO": "http://purl.obolibrary.org/obo/ExO_", "FAO": "http://purl.obolibrary.org/obo/FAO_", "FBSP": "http://purl.obolibrary.org/obo/FBSP_", "FBbi": "http://purl.obolibrary.org/obo/FBbi_", + "FIDEO": "http://purl.obolibrary.org/obo/FIDEO_", "FIX": "http://purl.obolibrary.org/obo/FIX_", "FLOPO": "http://purl.obolibrary.org/obo/FLOPO_", "FLU": "http://purl.obolibrary.org/obo/FLU_", "FMA": "http://purl.obolibrary.org/obo/FMA_", + "FOBI": "http://purl.obolibrary.org/obo/FOBI_", "FOODON": "http://purl.obolibrary.org/obo/FOODON_", + "FOVT": "http://purl.obolibrary.org/obo/FOVT_", "FYPO": "http://purl.obolibrary.org/obo/FYPO_", "GAZ": "http://purl.obolibrary.org/obo/GAZ_", + "GECKO": "http://purl.obolibrary.org/obo/GECKO_", "GENEPIO": "http://purl.obolibrary.org/obo/GENEPIO_", "GEO": "http://purl.obolibrary.org/obo/GEO_", + "GNO": "http://purl.obolibrary.org/obo/GNO_", "GRO": "http://purl.obolibrary.org/obo/GRO_", + "GSSO": "http://purl.obolibrary.org/obo/GSSO_", "HABRONATTUS": "http://purl.obolibrary.org/obo/HABRONATTUS_", + "HANCESTRO": "http://purl.obolibrary.org/obo/HANCESTRO_", "HAO": "http://purl.obolibrary.org/obo/HAO_", "HOM": "http://purl.obolibrary.org/obo/HOM_", - "HSAPDV": "http://purl.obolibrary.org/obo/HSAPDV_", + "HSO": "http://purl.obolibrary.org/obo/HSO_", + "HTN": "http://purl.obolibrary.org/obo/HTN_", + "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_", + "ICEO": "http://purl.obolibrary.org/obo/ICEO_", "ICO": "http://purl.obolibrary.org/obo/ICO_", "IDO": "http://purl.obolibrary.org/obo/IDO_", "IDOMAL": "http://purl.obolibrary.org/obo/IDOMAL_", "IEV": "http://purl.obolibrary.org/obo/IEV_", "IMR": "http://purl.obolibrary.org/obo/IMR_", + "INO": "http://purl.obolibrary.org/obo/INO_", "IPR": "http://purl.obolibrary.org/obo/IPR_", "KISAO": "http://purl.obolibrary.org/obo/KISAO_", + "LABO": "http://purl.obolibrary.org/obo/LABO_", "LIPRO": "http://purl.obolibrary.org/obo/LIPRO_", "LOGGERHEAD": "http://purl.obolibrary.org/obo/LOGGERHEAD_", "MAMO": "http://purl.obolibrary.org/obo/MAMO_", "MAO": "http://purl.obolibrary.org/obo/MAO_", "MAT": "http://purl.obolibrary.org/obo/MAT_", + "MAXO": "http://purl.obolibrary.org/obo/MAXO_", + "MCO": "http://purl.obolibrary.org/obo/MCO_", "MF": "http://purl.obolibrary.org/obo/MF_", "MFMO": "http://purl.obolibrary.org/obo/MFMO_", "MFO": "http://purl.obolibrary.org/obo/MFO_", @@ -877,18 +929,19 @@ "MIRNAO": "http://purl.obolibrary.org/obo/MIRNAO_", "MIRO": "http://purl.obolibrary.org/obo/MIRO_", "MMO": "http://purl.obolibrary.org/obo/MMO_", - "MMUSDV": "http://purl.obolibrary.org/obo/MMUSDV_", "MO": "http://purl.obolibrary.org/obo/MO_", "MOD": "http://purl.obolibrary.org/obo/MOD_", "MOP": "http://purl.obolibrary.org/obo/MOP_", "MPIO": "http://purl.obolibrary.org/obo/MPIO_", "MRO": "http://purl.obolibrary.org/obo/MRO_", "MS": "http://purl.obolibrary.org/obo/MS_", + "MmusDv": "http://purl.obolibrary.org/obo/MmusDv_", "NCRO": "http://purl.obolibrary.org/obo/NCRO_", "NIF_CELL": "http://purl.obolibrary.org/obo/NIF_CELL_", "NIF_DYSFUNCTION": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_", "NIF_GROSSANATOMY": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_", "NMR": "http://purl.obolibrary.org/obo/NMR_", + "NOMEN": "http://purl.obolibrary.org/obo/NOMEN_", "OARCS": "http://purl.obolibrary.org/obo/OARCS_", "OBCS": "http://purl.obolibrary.org/obo/OBCS_", "OBIB": "http://purl.obolibrary.org/obo/OBIB_", @@ -899,27 +952,38 @@ "OGSF": "http://purl.obolibrary.org/obo/OGSF_", "OHD": "http://purl.obolibrary.org/obo/OHD_", "OHMI": "http://purl.obolibrary.org/obo/OHMI_", - "OLATDV": "http://purl.obolibrary.org/obo/OLATDV_", + "OHPI": "http://purl.obolibrary.org/obo/OHPI_", "OMIABIS": "http://purl.obolibrary.org/obo/OMIABIS_", "OMIT": "http://purl.obolibrary.org/obo/OMIT_", + "OMO": "http://purl.obolibrary.org/obo/OMO_", "OMP": "http://purl.obolibrary.org/obo/OMP_", "OMRSE": "http://purl.obolibrary.org/obo/OMRSE_", + "ONE": "http://purl.obolibrary.org/obo/ONE_", + "ONS": "http://purl.obolibrary.org/obo/ONS_", "ONTONEO": "http://purl.obolibrary.org/obo/ONTONEO_", "OOSTT": "http://purl.obolibrary.org/obo/OOSTT_", "OPL": "http://purl.obolibrary.org/obo/OPL_", + "OPMI": "http://purl.obolibrary.org/obo/OPMI_", + "ORNASEQ": "http://purl.obolibrary.org/obo/ORNASEQ_", "OVAE": "http://purl.obolibrary.org/obo/OVAE_", + "OlatDv": "http://purl.obolibrary.org/obo/OlatDv_", "PAO": "http://purl.obolibrary.org/obo/PAO_", "PDRO": "http://purl.obolibrary.org/obo/PDRO_", - "PDUMDV": "http://purl.obolibrary.org/obo/PDUMDV_", "PD_ST": "http://purl.obolibrary.org/obo/PD_ST_", "PECO": "http://purl.obolibrary.org/obo/PECO_", "PGDSO": "http://purl.obolibrary.org/obo/PGDSO_", + "PHIPO": "http://purl.obolibrary.org/obo/PHIPO_", "PLANA": "http://purl.obolibrary.org/obo/PLANA_", + "PLANP": "http://purl.obolibrary.org/obo/PLANP_", "PLO": "http://purl.obolibrary.org/obo/PLO_", "PO": "http://purl.obolibrary.org/obo/PO_", "PORO": "http://purl.obolibrary.org/obo/PORO_", "PPO": "http://purl.obolibrary.org/obo/PPO_", "PROPREO": "http://purl.obolibrary.org/obo/PROPREO_", + "PSDO": "http://purl.obolibrary.org/obo/PSDO_", + "PSO": "http://purl.obolibrary.org/obo/PSO_", + "PdumDv": "http://purl.obolibrary.org/obo/PdumDv_", + "RBO": "http://purl.obolibrary.org/obo/RBO_", "RESID": "http://purl.obolibrary.org/obo/RESID_", "REX": "http://purl.obolibrary.org/obo/REX_", "RNAO": "http://purl.obolibrary.org/obo/RNAO_", @@ -927,6 +991,7 @@ "RXNO": "http://purl.obolibrary.org/obo/RXNO_", "SAO": "http://purl.obolibrary.org/obo/SAO_", "SBO": "http://purl.obolibrary.org/obo/SBO_", + "SCDO": "http://purl.obolibrary.org/obo/SCDO_", "SEP": "http://purl.obolibrary.org/obo/SEP_", "SIBO": "http://purl.obolibrary.org/obo/SIBO_", "SOPHARM": "http://purl.obolibrary.org/obo/SOPHARM_", @@ -942,14 +1007,15 @@ "TO": "http://purl.obolibrary.org/obo/TO_", "TRANS": "http://purl.obolibrary.org/obo/TRANS_", "TTO": "http://purl.obolibrary.org/obo/TTO_", + "TXPO": "http://purl.obolibrary.org/obo/TXPO_", + "UPA": "http://purl.obolibrary.org/obo/UPA_", "VARIO": "http://purl.obolibrary.org/obo/VARIO_", "VHOG": "http://purl.obolibrary.org/obo/VHOG_", "VO": "http://purl.obolibrary.org/obo/VO_", "VSAO": "http://purl.obolibrary.org/obo/VSAO_", "VTO": "http://purl.obolibrary.org/obo/VTO_", - "WBBT": "http://purl.obolibrary.org/obo/WBBT_", - "WBLS": "http://purl.obolibrary.org/obo/WBLS_", - "XL": "http://purl.obolibrary.org/obo/XL_", + "WBls": "http://purl.obolibrary.org/obo/WBls_", + "XLMOD": "http://purl.obolibrary.org/obo/XLMOD_", "YPO": "http://purl.obolibrary.org/obo/YPO_", "ZEA": "http://purl.obolibrary.org/obo/ZEA_", "ZECO": "http://purl.obolibrary.org/obo/ZECO_" diff --git a/registry/idot_nr_context.jsonld b/registry/idot_nr_context.jsonld index 8e87355..85dbc74 100644 --- a/registry/idot_nr_context.jsonld +++ b/registry/idot_nr_context.jsonld @@ -456,7 +456,7 @@ "NONCODEV4.GENE": "http://identifiers.org/noncodev4.gene/", "WIKIGENES": "http://identifiers.org/wikigenes/", "GWASCENTRAL.STUDY": "http://identifiers.org/gwascentral.study/", - "NCBIGENE": "http://identifiers.org/ncbigene/", + "NCBIGene": "http://identifiers.org/ncbigene/", "GRID": "http://identifiers.org/grid/", "SIDER.EFFECT": "http://identifiers.org/sider.effect/", "EXAC.VARIANT": "http://identifiers.org/exac.variant/", diff --git a/registry/monarch_context.jsonld b/registry/monarch_context.jsonld index e42af1d..d47fa04 100644 --- a/registry/monarch_context.jsonld +++ b/registry/monarch_context.jsonld @@ -5,12 +5,15 @@ "APO": "http://purl.obolibrary.org/obo/APO_", "AQTLPub": "https://www.animalgenome.org/cgi-bin/QTLdb/BT/qabstract?PUBMED_ID=", "AQTLTrait": "http://identifiers.org/animalqtltrait/", + "AspGD": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=", + "AspGD_REF": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=", "BFO": "http://purl.obolibrary.org/obo/BFO_", + "BGD": "http://bovinegenome.org/genepages/btau40/genes/", "BIOGRID": "http://thebiogrid.org/", - "biolink" : "https://w3id.org/biolink/vocab/", "BNODE": "https://monarchinitiative.org/.well-known/genid/", "BT": "http://c.biothings.io/#", "CCDS": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=", + "CGNC": "http://birdgenenames.org/cgnc/GeneReport?id=", "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", "CHR": "http://purl.obolibrary.org/obo/CHR_", "CID": "http://pubchem.ncbi.nlm.nih.gov/compound/", @@ -18,66 +21,78 @@ "CLO": "http://purl.obolibrary.org/obo/CLO_", "CMMR": "http://www.cmmr.ca/order.php?t=m&id=", "CMO": "http://purl.obolibrary.org/obo/CMO_", + "COHD": "http://purl.obolibrary.org/obo/COHD_", "COSMIC": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=", "ClinVar": "http://www.ncbi.nlm.nih.gov/clinvar/", "ClinVarSubmitters": "http://www.ncbi.nlm.nih.gov/clinvar/submitters/", "ClinVarVariant": "http://www.ncbi.nlm.nih.gov/clinvar/variation/", + "ComplexPortal": "https://www.ebi.ac.uk/complexportal/complex/", "Coriell": "https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=", "CoriellCollection": "https://catalog.coriell.org/1/", "CoriellFamily": "https://catalog.coriell.org/0/Sections/BrowseCatalog/FamilyTypeSubDetail.aspx?fam=", "CoriellIndividual": "https://catalog.coriell.org/Search?q=", - "DATA": "http://edamontology.org/data_", "DC_CL": "http://purl.obolibrary.org/obo/DC_CL", - "DECIPHER": "http://purl.obolibrary.org/obo/DECIPHER_", + "DECIPHER": "https://decipher.sanger.ac.uk/syndrome/", "DOI": "http://dx.doi.org/", "DOID": "http://purl.obolibrary.org/obo/DOID_", "DrugBank": "http://www.drugbank.ca/drugs/", - "EC": "http://www.enzyme-database.org/query.php?ec=", + "EC": "https://www.enzyme-database.org/query.php?ec=", "ECO": "http://purl.obolibrary.org/obo/ECO_", - "EFO": "http://purl.obolibrary.org/obo/EFO_", + "EDAM-DATA": "http://edamontology.org/data_", + "EFO": "http://www.ebi.ac.uk/efo/EFO_", "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", "EMMA": "https://www.infrafrontier.eu/search?keyword=EM:", "ENSEMBL": "http://ensembl.org/id/", "ENVO": "http://purl.obolibrary.org/obo/ENVO_", - "EOM": "http://purl.obolibrary.org/obo/EOM_", + "EOM": "https://elementsofmorphology.nih.gov/index.cgi?tid=", + "EOM_IMG": "https://elementsofmorphology.nih.gov/images/terms/", "ERO": "http://purl.obolibrary.org/obo/ERO_", "EcoGene": "http://ecogene.org/gene/", + "EnsemblGenome": "http://www.ensemblgenomes.org/id/", "FBbt": "http://purl.obolibrary.org/obo/FBbt_", "FBcv": "http://purl.obolibrary.org/obo/FBcv_", "FBdv": "http://purl.obolibrary.org/obo/FBdv_", "FDADrug": "http://www.fda.gov/Drugs/InformationOnDrugs/", "FlyBase": "http://flybase.org/reports/", + "GARD": "http://purl.obolibrary.org/obo/GARD_", "GENO": "http://purl.obolibrary.org/obo/GENO_", "GINAS": "http://tripod.nih.gov/ginas/app/substance#", "GO": "http://purl.obolibrary.org/obo/GO_", "GO_REF": "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:", + "GWAS": "https://www.ebi.ac.uk/gwas/variants/", "GenBank": "http://www.ncbi.nlm.nih.gov/nuccore/", + "Genatlas": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=", "GeneReviews": "http://www.ncbi.nlm.nih.gov/books/", "HGMD": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=", - "HGNC": "http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=", + "HGNC": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:", "HMDB": "http://www.hmdb.ca/metabolites/", "HOMOLOGENE": "http://www.ncbi.nlm.nih.gov/homologene/", "HP": "http://purl.obolibrary.org/obo/HP_", "HPO": "http://human-phenotype-ontology.org/", "HPRD": "http://www.hprd.org/protein/", "IAO": "http://purl.obolibrary.org/obo/IAO_", - "IMPC": "http://www.mousephenotype.org/data/genes/", - "IMPRESS-parameter": "https://www.mousephenotype.org/impress/parameterontologies/", - "IMPRESS-procedure": "https://www.mousephenotype.org/impress/procedures/", - "IMPRESS-protocol": "https://www.mousephenotype.org/impress/protocol/", + "ICD9": "http://purl.obolibrary.org/obo/ICD9_", + "IMPC": "https://www.mousephenotype.org/data/genes/", + "IMPC-param": "https://www.mousephenotype.org/impress/OntologyInfo?action=list&procID=", + "IMPC-pipe": "https://www.mousephenotype.org/impress/PipelineInfo?id=", + "IMPC-proc": "https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=", "ISBN": "https://monarchinitiative.org/ISBN_", "ISBN-10": "https://monarchinitiative.org/ISBN10_", "ISBN-13": "https://monarchinitiative.org/ISBN13_", + "IUPHAR": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=", + "InterPro": "https://www.ebi.ac.uk/interpro/entry/InterPro/", "J": "http://www.informatics.jax.org/reference/J:", "JAX": "http://jaxmice.jax.org/strain/", "KEGG-ds": "http://purl.obolibrary.org/KEGG-ds_", "KEGG-hsa": "http://www.kegg.jp/dbget-bin/www_bget?hsa:", + "KEGG-img": "http://www.genome.jp/kegg/pathway/map/", "KEGG-ko": "http://www.kegg.jp/dbget-bin/www_bget?ko:", "KEGG-path": "http://www.kegg.jp/dbget-bin/www_bget?path:", + "LIDA": "http://sydney.edu.au/vetscience/lida/dogs/search/disorder/", "LPT": "http://purl.obolibrary.org/obo/LPT_", "MA": "http://purl.obolibrary.org/obo/MA_", "MEDDRA": "http://purl.bioontology.org/ontology/MEDDRA/", - "MESH": "http://purl.obolibrary.org/obo/MESH_", + "MESH": "http://id.nlm.nih.gov/mesh/", "MGI": "http://www.informatics.jax.org/accession/MGI:", "MMRRC": "https://www.mmrrc.org/catalog/sds.php?mmrrc_id=", "MONARCH": "https://monarchinitiative.org/MONARCH_", @@ -89,12 +104,14 @@ "MPD-strain": "http://phenome.jax.org/db/q?rtn=strains/details&strainid=", "MUGEN": "http://bioit.fleming.gr/mugen/Controller?workflow=ViewModel&expand_all=true&name_begins=model.block&eid=", "MedGen": "http://www.ncbi.nlm.nih.gov/medgen/", - "MonarchArchive": "https://archive.monarchinitiative.org/201806/", + "MonarchArchive": "https://archive.monarchinitiative.org/", "MonarchData": "https://data.monarchinitiative.org/ttl/", + "MonarchLogoRepo": "https://github.com/monarch-initiative/monarch-ui/blob/master/public/img/sources/", "NBO": "http://purl.obolibrary.org/obo/NBO_", - "NCBIAssembly": "http://www.ncbi.nlm.nih.gov/assembly/", - "NCBIGene": "http://www.ncbi.nlm.nih.gov/gene/", - "NCBIGenome": "http://www.ncbi.nlm.nih.gov/genome/", + "NCBIAssembly": "https://www.ncbi.nlm.nih.gov/assembly?term=", + "NCBIBSgene": "http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=", + "NCBIGene": "https://www.ncbi.nlm.nih.gov/gene/", + "NCBIGenome": "https://www.ncbi.nlm.nih.gov/genome/", "NCBIProtein": "http://www.ncbi.nlm.nih.gov/protein/", "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", "NCIMR": "https://mouse.ncifcrf.gov/available_details.asp?ID=", @@ -104,11 +121,11 @@ "OBAN": "http://purl.org/oban/", "OBI": "http://purl.obolibrary.org/obo/OBI_", "OBO": "http://purl.obolibrary.org/obo/", - "OIO": "http://www.geneontology.org/formats/oboInOwl#", - "OMIA": "http://purl.obolibrary.org/obo/OMIA_", + "OMIA": "https://omia.org/OMIA", "OMIA-breed": "https://monarchinitiative.org/model/OMIA-breed:", - "OMIM": "http://purl.obolibrary.org/obo/OMIM_", - "Orphanet": "http://www.orpha.net/ORDO/Orphanet_", + "OMIM": "http://omim.org/entry/", + "OMIMPS": "http://www.omim.org/phenotypicSeries/", + "ORPHA": "http://www.orpha.net/ORDO/Orphanet_", "PAINT_REF": "http://www.geneontology.org/gene-associations/submission/paint/", "PANTHER": "http://www.pantherdb.org/panther/family.do?clsAccession=", "PATO": "http://purl.obolibrary.org/obo/PATO_", @@ -119,13 +136,14 @@ "PR": "http://purl.obolibrary.org/obo/PR_", "PW": "http://purl.obolibrary.org/obo/PW_", "PomBase": "https://www.pombase.org/spombe/result/", - "RBRC": "http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=RBRC", + "RBRC": "http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=", "REACT": "http://www.reactome.org/PathwayBrowser/#/", "RGD": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=", "RGDRef": "http://rgd.mcw.edu/rgdweb/report/reference/main.html?id=", "RO": "http://purl.obolibrary.org/obo/RO_", "RXCUI": "http://purl.bioontology.org/ontology/RXNORM/", "RefSeq": "http://www.ncbi.nlm.nih.gov/refseq/?term=", + "SCTID": "http://purl.obolibrary.org/obo/SCTID_", "SEPIO": "http://purl.obolibrary.org/obo/SEPIO_", "SGD": "https://www.yeastgenome.org/locus/", "SGD_REF": "https://www.yeastgenome.org/reference/", @@ -139,11 +157,13 @@ "TrEMBL": "http://purl.uniprot.org/uniprot/", "UBERON": "http://purl.obolibrary.org/obo/UBERON_", "UCSC": "ftp://hgdownload.cse.ucsc.edu/goldenPath/", + "UCSCBuild": "http://genome.ucsc.edu/cgi-bin/hgGateway?db=", "UMLS": "http://linkedlifedata.com/resource/umls/id/", "UNII": "http://fdasis.nlm.nih.gov/srs/unii/", "UO": "http://purl.obolibrary.org/obo/UO_", "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", "UniProtKB": "http://identifiers.org/uniprot/", + "VGNC": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/", "VIVO": "http://vivoweb.org/ontology/core#", "VT": "http://purl.obolibrary.org/obo/VT_", "WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_", @@ -153,33 +173,40 @@ "WormBase": "https://www.wormbase.org/get?name=", "XAO": "http://purl.obolibrary.org/obo/XAO_", "XCO": "http://purl.obolibrary.org/obo/XCO_", - "Xenbase": "http://www.xenbase.org/gene/showgene.do?method=display&geneId=", + "XPO": "http://purl.obolibrary.org/obo/XPO_", + "Xenbase": "http://identifiers.org/xenbase/", "ZFA": "http://purl.obolibrary.org/obo/ZFA_", "ZFIN": "http://zfin.org/", "ZFS": "http://purl.obolibrary.org/obo/ZFS_", "ZP": "http://purl.obolibrary.org/obo/ZP_", + "biolink": "https://w3id.org/biolink/vocab/", "catfishQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/IP/qdetails?QTL_ID=", - "cattleQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_D=", + "cattleQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=", "chickenQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=", + "cito": "http://purl.org/spar/cito/", "dbSNP": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=", "dbSNPIndividual": "http://www.ncbi.nlm.nih.gov/SNP/snp_ind.cgi?ind_id=", "dbVar": "http://www.ncbi.nlm.nih.gov/dbvar/", - "dc": "http://purl.org/dc/elements/1.1/", + "dc": "http://purl.org/dc/terms/", "dcat": "http://www.w3.org/ns/dcat#", - "dcterms": "http://purl.org/dc/terms/", "dctypes": "http://purl.org/dc/dcmitype/", "dictyBase": "http://dictybase.org/gene/", "faldo": "http://biohackathon.org/resource/faldo#", "foaf": "http://xmlns.com/foaf/0.1/", "horseQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/EC/qdetails?QTL_ID=", + "miRBase": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=", + "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", "owl": "http://www.w3.org/2002/07/owl#", "pav": "http://purl.org/pav/", "pigQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=", "rainbow_troutQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/OM/qdetails?QTL_ID=", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "schema": "http://schema.org/", "sheepQTL": "https://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=", - "skos": "https://www.w3.org/TR/skos-reference/#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "vfb": "http://virtualflybrain.org/reports/", + "void": "http://rdfs.org/ns/void#", "xml": "http://www.w3.org/XML/1998/namespace", "xsd": "http://www.w3.org/2001/XMLSchema#" } diff --git a/reports/clashes.txt b/reports/clashes.txt index 6620418..9d9e234 100644 --- a/reports/clashes.txt +++ b/reports/clashes.txt @@ -60,6 +60,7 @@ WARNING:root:URI clash: http://mged.sourceforge.net/ontologies/MGEDontology.php# WARNING:root:Prefix clash: MO Was=http://mged.sourceforge.net/ontologies/MGEDontology.php# [registry/go_context.jsonld], Now=http://identifiers.org/mo/ [registry/idot_context.jsonld] WARNING:root:URI clash: https://www.worldcat.org/search?q=bn%3A is expansion for ISBN and ISBN WARNING:root:Prefix clash: ISBN Was=https://www.worldcat.org/search?q=bn%3A [registry/go_context.jsonld], Now=http://identifiers.org/isbn/ [registry/idot_context.jsonld] +WARNING:root:URI clash: http://identifiers.org/ncbigene/ is expansion for NCBIGene and NCBIGene WARNING:root:URI clash: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref= is expansion for CORIELL and CORIELL WARNING:root:Prefix clash: CORIELL Was=http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref= [registry/go_context.jsonld], Now=http://identifiers.org/coriell/ [registry/idot_context.jsonld] WARNING:root:URI clash: http://purl.obolibrary.org/obo/FMA_ is expansion for FMA and FMA @@ -70,8 +71,7 @@ WARNING:root:URI clash: http://purl.obolibrary.org/obo/GO_ is expansion for GO a WARNING:root:Prefix clash: GO Was=http://purl.obolibrary.org/obo/GO_ [registry/go_context.jsonld], Now=http://identifiers.org/go/ [registry/idot_context.jsonld] WARNING:root:URI clash: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId= is expansion for PDB and PDB WARNING:root:Prefix clash: PDB Was=http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId= [registry/go_context.jsonld], Now=http://identifiers.org/pdb/ [registry/idot_context.jsonld] -WARNING:root:URI clash: http://identifiers.org/mgi/MGI: is expansion for MGI and MGI -WARNING:root:Prefix clash: MGI Was=http://identifiers.org/mgi/MGI: [registry/go_context.jsonld], Now=http://identifiers.org/mgi/ [registry/idot_context.jsonld] +WARNING:root:URI clash: http://identifiers.org/mgi/ is expansion for MGI and MGI WARNING:root:URI clash: http://identifiers.org/sgn/ is expansion for SGN and SGN WARNING:root:URI clash: http://identifiers.org/cgd/ is expansion for CGD and CGD WARNING:root:URI clash: http://hamap.expasy.org/unirule/ is expansion for HAMAP and HAMAP @@ -83,18 +83,21 @@ WARNING:root:URI clash: http://purl.obolibrary.org/obo/PR_ is expansion for PR a WARNING:root:Prefix clash: PR Was=http://purl.obolibrary.org/obo/PR_ [registry/go_context.jsonld], Now=http://identifiers.org/pr/ [registry/idot_context.jsonld] WARNING:root:URI clash: http://www.brenda-enzymes.info/php/result_flat.php4?ecno= is expansion for BRENDA and BRENDA WARNING:root:Prefix clash: BRENDA Was=http://www.brenda-enzymes.info/php/result_flat.php4?ecno= [registry/go_context.jsonld], Now=http://identifiers.org/brenda/ [registry/idot_context.jsonld] +WARNING:root:URI clash: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid= is expansion for AspGD and AspGD +WARNING:root:URI clash: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid= is expansion for AspGD_REF and AspGD_REF WARNING:root:URI clash: http://purl.obolibrary.org/obo/BFO_ is expansion for BFO and BFO WARNING:root:Prefix clash: BIOGRID Was=http://identifiers.org/biogrid/ [registry/idot_context.jsonld], Now=http://thebiogrid.org/ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: CCDS Was=http://identifiers.org/ccds/ [registry/idot_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA= [registry/monarch_context.jsonld] WARNING:root:Prefix clash: CHEBI Was=http://identifiers.org/chebi/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/CHEBI_ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: CL Was=http://identifiers.org/cl/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/CL_ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: COSMIC Was=http://identifiers.org/cosmic/ [registry/idot_context.jsonld], Now=http://cancer.sanger.ac.uk/cosmic/mutation/overview?id= [registry/monarch_context.jsonld] +WARNING:root:URI clash: https://www.ebi.ac.uk/complexportal/complex/ is expansion for ComplexPortal and ComplexPortal WARNING:root:Prefix clash: DOI Was=http://identifiers.org/doi/ [registry/idot_context.jsonld], Now=http://dx.doi.org/ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: DOID Was=http://identifiers.org/doid/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/DOID_ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://www.expasy.org/enzyme/ is expansion for EC and EC -WARNING:root:Prefix clash: EC Was=http://www.expasy.org/enzyme/ [registry/go_context.jsonld], Now=http://www.enzyme-database.org/query.php?ec= [registry/monarch_context.jsonld] +WARNING:root:Prefix clash: EC Was=http://www.expasy.org/enzyme/ [registry/go_context.jsonld], Now=https://www.enzyme-database.org/query.php?ec= [registry/monarch_context.jsonld] WARNING:root:Prefix clash: ECO Was=http://identifiers.org/eco/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/ECO_ [registry/monarch_context.jsonld] -WARNING:root:Prefix clash: EFO Was=http://identifiers.org/efo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/EFO_ [registry/monarch_context.jsonld] +WARNING:root:Prefix clash: EFO Was=http://identifiers.org/efo/ [registry/idot_context.jsonld], Now=http://www.ebi.ac.uk/efo/EFO_ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://purl.obolibrary.org/obo/EMAPA_ is expansion for EMAPA and EMAPA WARNING:root:URI clash: http://identifiers.org/ensembl/ is expansion for ENSEMBL and ENSEMBL WARNING:root:Prefix clash: ENSEMBL Was=http://identifiers.org/ensembl/ [registry/idot_context.jsonld], Now=http://ensembl.org/id/ [registry/monarch_context.jsonld] @@ -107,27 +110,29 @@ WARNING:root:URI clash: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleo WARNING:root:Prefix clash: GenBank Was=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val= [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/nuccore/ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: HGMD Was=http://identifiers.org/hgmd/ [registry/idot_context.jsonld], Now=http://www.hgmd.cf.ac.uk/ac/gene.php?gene= [registry/monarch_context.jsonld] WARNING:root:URI clash: http://identifiers.org/hgnc/ is expansion for HGNC and HGNC -WARNING:root:Prefix clash: HGNC Was=http://identifiers.org/hgnc/ [registry/idot_context.jsonld], Now=http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id= [registry/monarch_context.jsonld] +WARNING:root:Prefix clash: HGNC Was=http://identifiers.org/hgnc/ [registry/idot_context.jsonld], Now=https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC: [registry/monarch_context.jsonld] WARNING:root:Prefix clash: HMDB Was=http://identifiers.org/hmdb/ [registry/idot_context.jsonld], Now=http://www.hmdb.ca/metabolites/ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: HOMOLOGENE Was=http://identifiers.org/homologene/ [registry/idot_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/homologene/ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: HP Was=http://identifiers.org/hp/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/HP_ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: HPRD Was=http://identifiers.org/hprd/ [registry/idot_context.jsonld], Now=http://www.hprd.org/protein/ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: IAO Was=http://identifiers.org/iao/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/IAO_ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: ISBN Was=http://identifiers.org/isbn/ [registry/idot_context.jsonld], Now=https://monarchinitiative.org/ISBN_ [registry/monarch_context.jsonld] +WARNING:root:URI clash: http://identifiers.org/interpro/ is expansion for InterPro and InterPro +WARNING:root:Prefix clash: InterPro Was=http://identifiers.org/interpro/ [registry/go_context.jsonld], Now=https://www.ebi.ac.uk/interpro/entry/InterPro/ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: MA Was=http://identifiers.org/ma/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MA_ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: MEDDRA Was=http://identifiers.org/meddra/ [registry/idot_context.jsonld], Now=http://purl.bioontology.org/ontology/MEDDRA/ [registry/monarch_context.jsonld] -WARNING:root:Prefix clash: MESH Was=http://identifiers.org/mesh/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MESH_ [registry/monarch_context.jsonld] +WARNING:root:Prefix clash: MESH Was=http://identifiers.org/mesh/ [registry/idot_context.jsonld], Now=http://id.nlm.nih.gov/mesh/ [registry/monarch_context.jsonld] +WARNING:root:URI clash: http://identifiers.org/mgi/ is expansion for MGI and MGI WARNING:root:Prefix clash: MGI Was=http://identifiers.org/mgi/ [registry/idot_context.jsonld], Now=http://www.informatics.jax.org/accession/MGI: [registry/monarch_context.jsonld] WARNING:root:Prefix clash: MMRRC Was=http://identifiers.org/mmrrc/ [registry/idot_context.jsonld], Now=https://www.mmrrc.org/catalog/sds.php?mmrrc_id= [registry/monarch_context.jsonld] WARNING:root:Prefix clash: MP Was=http://identifiers.org/mp/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MP_ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://identifiers.org/ncbigene/ is expansion for NCBIGene and NCBIGene -WARNING:root:Prefix clash: NCBIGene Was=http://identifiers.org/ncbigene/ [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/gene/ [registry/monarch_context.jsonld] +WARNING:root:Prefix clash: NCBIGene Was=http://identifiers.org/ncbigene/ [registry/idot_context.jsonld], Now=https://www.ncbi.nlm.nih.gov/gene/ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://purl.obolibrary.org/obo/NCBITaxon_ is expansion for NCBITaxon and NCBITaxon WARNING:root:Prefix clash: NCIT Was=http://identifiers.org/ncit/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/NCIT_ [registry/monarch_context.jsonld] WARNING:root:Prefix clash: OBI Was=http://identifiers.org/obi/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/OBI_ [registry/monarch_context.jsonld] -WARNING:root:Prefix clash: OMIA Was=http://identifiers.org/omia/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/OMIA_ [registry/monarch_context.jsonld] +WARNING:root:Prefix clash: OMIA Was=http://identifiers.org/omia/ [registry/idot_context.jsonld], Now=https://omia.org/OMIA [registry/monarch_context.jsonld] WARNING:root:URI clash: http://omim.org/entry/ is expansion for OMIM and OMIM -WARNING:root:Prefix clash: OMIM Was=http://omim.org/entry/ [registry/go_context.jsonld], Now=http://purl.obolibrary.org/obo/OMIM_ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR is expansion for PAINT_REF and PAINT_REF WARNING:root:Prefix clash: PAINT_REF Was=http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR [registry/go_context.jsonld], Now=http://www.geneontology.org/gene-associations/submission/paint/ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://identifiers.org/panther.family/ is expansion for PANTHER and PANTHER @@ -159,17 +164,14 @@ WARNING:root:Prefix clash: UO Was=http://identifiers.org/uo/ [registry/idot_cont WARNING:root:URI clash: http://identifiers.org/uniprot/ is expansion for UniProtKB and UniProtKB WARNING:root:URI clash: http://purl.obolibrary.org/obo/WBPhenotype_ is expansion for WBPhenotype and WBPhenotype WARNING:root:URI clash: http://identifiers.org/xenbase/ is expansion for Xenbase and Xenbase -WARNING:root:Prefix clash: Xenbase Was=http://identifiers.org/xenbase/ [registry/go_context.jsonld], Now=http://www.xenbase.org/gene/showgene.do?method=display&geneId= [registry/monarch_context.jsonld] WARNING:root:URI clash: http://identifiers.org/zfin/ is expansion for ZFIN and ZFIN WARNING:root:Prefix clash: ZFIN Was=http://identifiers.org/zfin/ [registry/idot_context.jsonld], Now=http://zfin.org/ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://identifiers.org/dbsnp/ is expansion for dbSNP and dbSNP WARNING:root:Prefix clash: dbSNP Was=http://identifiers.org/dbsnp/ [registry/go_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs= [registry/monarch_context.jsonld] -WARNING:root:Prefix clash: dc Was=http://purl.org/dc/terms/ [registry/semweb_context.jsonld], Now=http://purl.org/dc/elements/1.1/ [registry/monarch_context.jsonld] -WARNING:root:URI clash: http://purl.org/dc/terms/ is expansion for dcterms and dc WARNING:root:URI clash: http://identifiers.org/dictybase.gene/ is expansion for dictyBase and dictyBase WARNING:root:Prefix clash: dictyBase Was=http://identifiers.org/dictybase.gene/ [registry/go_context.jsonld], Now=http://dictybase.org/gene/ [registry/monarch_context.jsonld] WARNING:root:URI clash: http://www.w3.org/2001/XMLSchema# is expansion for xsd and xsd -WARNING:root:Prefix clash: dc Was=http://purl.org/dc/elements/1.1/ [registry/monarch_context.jsonld], Now=http://purl.org/dc/terms/ [registry/semweb_vocab_context.jsonld] +WARNING:root:URI clash: http://purl.org/dc/terms/ is expansion for dc and dc WARNING:root:URI clash: http://www.w3.org/ns/dcat# is expansion for dcat and dcat WARNING:root:URI clash: http://www.w3.org/2002/07/owl# is expansion for owl and owl WARNING:root:URI clash: http://xmlns.com/foaf/0.1/ is expansion for foaf and foaf @@ -211,3 +213,4 @@ WARNING:root:URI clash: http://purl.obolibrary.org/obo/SO_ is expansion for SO a WARNING:root:URI clash: http://purl.obolibrary.org/obo/UBERON_ is expansion for UBERON and UBERON WARNING:root:Prefix clash: VARIO Was=http://identifiers.org/vario/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/VARIO_ [registry/obo_context.jsonld] WARNING:root:URI clash: http://purl.obolibrary.org/obo/WBPhenotype_ is expansion for WBPhenotype and WBPhenotype +WARNING:root:URI clash: http://purl.obolibrary.org/obo/WBls_ is expansion for WBls and WBls