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update obo context, make a hard coded change for NCBIGene #37

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update obo context, make a hard coded change for NCBIGene #37

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632f86e
fix NCBIGene for biolink-model
sierra-moxon May 20, 2021
a0255f1
update obo_context
sierra-moxon May 21, 2021
91ee300
update travis to use newer version of python
sierra-moxon May 21, 2021
e29c4ba
update obo context
sierra-moxon May 21, 2021
a51ec76
get makefile working
sierra-moxon May 21, 2021
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2 changes: 1 addition & 1 deletion .travis.yml
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@@ -1,6 +1,6 @@
language: python
python:
- "3.4"
- "3.7"

# command to install dependencies
install:
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12 changes: 6 additions & 6 deletions Makefile
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Expand Up @@ -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:
Expand All @@ -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
##
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132 changes: 99 additions & 33 deletions registry/commons_context.jsonld
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2 changes: 1 addition & 1 deletion registry/idot_context.jsonld
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Expand Up @@ -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/",
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2 changes: 1 addition & 1 deletion registry/idot_nr_context.jsonld
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Expand Up @@ -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/",
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79 changes: 53 additions & 26 deletions registry/monarch_context.jsonld
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Expand Up @@ -5,79 +5,94 @@
"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/",
"CL": "http://purl.obolibrary.org/obo/CL_",
"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_",
Expand All @@ -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=",
Expand All @@ -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_",
Expand All @@ -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/",
Expand All @@ -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_",
Expand All @@ -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#"
}
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