From bad66e0e8f4abe08c48e4fb5db938c6c1ba78175 Mon Sep 17 00:00:00 2001 From: cmungall Date: Thu, 19 Apr 2018 14:43:25 -0700 Subject: [PATCH 1/4] Adding goxrefs_context.jsonld This is a derived copy of the central GO db-xrefs.yaml file See: https://github.com/geneontology/go-site/issues/617 --- registry/goxrefs_context.jsonld | 216 ++++++++++++++++++++++++++++++++ 1 file changed, 216 insertions(+) create mode 100644 registry/goxrefs_context.jsonld diff --git a/registry/goxrefs_context.jsonld b/registry/goxrefs_context.jsonld new file mode 100644 index 0000000..3ef16c0 --- /dev/null +++ b/registry/goxrefs_context.jsonld @@ -0,0 +1,216 @@ +{ + "@context": { + "BIOMD": "http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=", + "COG_Function": "http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=", + "WB": "http://identifiers.org/wormbase/", + "FBbt": "http://purl.obolibrary.org/obo/FBbt_", + "KEGG_LIGAND": "http://www.genome.jp/dbget-bin/www_bget?cpd:", + "PSO_GIT": "https://github.com/Planteome/plant-stress-ontology/issues/", + "MaizeGDB_stock": "http://maizegdb.org/data_center/stock?id=", + "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", + "GO": "http://purl.obolibrary.org/obo/GO_", + "NCBI_GP": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=", + "NMPDR": "http://www.nmpdr.org/linkin.cgi?id=", + "CASSPC": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=", + "TGD_REF": "http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=", + "NCBIGene": "http://identifiers.org/ncbigene/", + "KEGG_REACTION": "http://www.genome.jp/dbget-bin/www_bget?rn:", + "PseudoCAP": "http://v2.pseudomonas.com/getAnnotation.do?locusID=", + "UniPathway": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", + "MEROPS_fam": "http://merops.sanger.ac.uk/cgi-bin/famsum?family=", + "GO_REF": "http://purl.obolibrary.org/obo/go/references/", + "VEGA": "http://vega.sanger.ac.uk/id/", + "EnsemblProtists": "http://www.ensemblgenomes.org/id/", + "ZFIN": "http://identifiers.org/zfin/", + "AspGD_REF": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=", + "RO": "http://purl.obolibrary.org/obo/RO_", + "Pfam": "http://pfam.xfam.org/family/", + "UBERON": "http://purl.obolibrary.org/obo/UBERON_", + "GR": "http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=", + "PDB": "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=", + "CORIELL": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=", + "JCVI_GenProp": "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=", + "SGN": "http://identifiers.org/sgn/", + "BFO": "http://purl.obolibrary.org/obo/BFO_", + "Genesys-pgr": "https://www.genesys-pgr.org/acn/search?q=", + "NCBI_gi": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=", + "UniMod": "http://www.unimod.org/modifications_view.php?editid1=", + "UM-BBD_reactionID": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=", + "PubChem_Substance": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=", + "EcoCyc": "http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=", + "Reactome": "http://identifiers.org/reactome/", + "InterPro": "http://identifiers.org/interpro/", + "UniRule": "http://www.uniprot.org/unirule/", + "MGCSC_GENETIC_STOCKS": "http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=", + "dictyBase": "http://identifiers.org/dbsnp/", + "PO_GIT": "https://github.com/Planteome/plant-ontology/issues/", + "AspGD_LOCUS": "http://identifiers.org/aspgd.locus/", + "SGD": "http://identifiers.org/sgd/", + "COG_Pathway": "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=", + "ENZYME": "http://www.expasy.ch/cgi-bin/nicezyme.pl?", + "PAMGO_MGG": "http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=", + "AgBase": "http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=", + "AraCyc": "http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=", + "GONUTS": "http://gowiki.tamu.edu/wiki/index.php/", + "EcoCyc_REF": "http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=", + "EnsemblPlants": "http://www.ensemblgenomes.org/id/", + "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", + "HGNC": "http://identifiers.org/hgnc/", + "dictyBase_gene_name": "http://dictybase.org/gene/", + "ENSEMBL_ProteinID": "http://www.ensembl.org/id/", + "TAIR": "http://identifiers.org/tair.locus/", + "EnsemblFungi": "http://www.ensemblgenomes.org/id/", + "Wikipedia": "http://en.wikipedia.org/wiki/", + "SUPERFAMILY": "http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF", + "SWALL": "http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=", + "PSI-MOD": "http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:", + "FYPO": "http://purl.obolibrary.org/obo/FYPO_", + "RGD": "http://identifiers.org/rgd/", + "UM-BBD_enzymeID": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=", + "Broad_MGG": "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S", + "Swiss-Prot": "http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=", + "PMID": "http://www.ncbi.nlm.nih.gov/pubmed/", + "Xenbase": "http://identifiers.org/xenbase/", + "PR": "http://purl.obolibrary.org/obo/PR_", + "MIPS_funcat": "http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=", + "GR_REF": "http://www.gramene.org/db/literature/pub_search?ref_id=", + "MaizeGDB": "http://maizegdb.org/gene_center/gene/", + "EnsemblMetazoa": "http://www.ensemblgenomes.org/id/", + "HAMAP": "http://hamap.expasy.org/unirule/", + "SGN_ref": "http://www.sgn.cornell.edu/chado/publication.pl?pub_id=", + "TO_GIT": "https://github.com/Planteome/plant-trait-ontology/issues/", + "MeSH": "http://n2t.net/MESH:", + "GR_PROTEIN": "http://identifiers.org/gramene.protein/", + "MaizeGDB_REF": "http://maizegdb.org/data_center/reference?id=", + "GEO": "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=", + "PO": "http://purl.obolibrary.org/obo/PO_", + "ENSEMBL_TranscriptID": "http://www.ensembl.org/id/", + "PomBase": "http://identifiers.org/pombase/", + "ENA": "http://www.ebi.ac.uk/ena/data/view/", + "PIRSF": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=", + "EMBL": "http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=", + "Prosite": "http://www.expasy.ch/cgi-bin/prosite-search-ac?", + "H-invDB_cDNA": "http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=", + "EC": "http://www.expasy.org/enzyme/", + "MACSC_REF": "http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=", + "PAMGO_VMD": "http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=", + "IRGC": "https://www.genesys-pgr.org/acn/search?q=IRGC+", + "NASC_code": "http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=", + "COG_Cluster": "http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=", + "TreeGenes": "http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=", + "WB_REF": "http://www.wormbase.org/db/misc/paper?name=", + "TGD_LOCUS": "http://db.ciliate.org/cgi-bin/locus.pl?locus=", + "MA": "http://purl.obolibrary.org/obo/MA_", + "MGI": "http://identifiers.org/mgi/", + "GRINDesc": "https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=", + "DDANAT": "http://purl.obolibrary.org/obo/DDANAT_", + "RAP-DB": "http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=", + "KEGG_PATHWAY": "http://identifiers.org/kegg.pathway/", + "JCVI_CMR": "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=", + "dictyBase_REF": "http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=", + "DOI": "http://dx.doi.org/", + "LIFEdb": "http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=", + "PANTHER": "http://identifiers.org/panther.family/", + "Gene3D": "http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=", + "PATRIC": "http://patric.vbi.vt.edu/gene/overview.php?fid=", + "FB": "http://identifiers.org/flybase/", + "UniProtKB": "http://identifiers.org/uniprot/", + "CASREF": "http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=", + "ENSEMBL": "http://identifiers.org/ensembl/", + "SMART": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=", + "RefSeq": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=", + "WBls": "http://purl.obolibrary.org/obo/WBls_", + "MaizeGDB_QTL": "http://www.maizegdb.org/data_center/trait?id=", + "SOY_ref": "http://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=", + "ECO": "http://purl.obolibrary.org/obo/ECO_", + "CGD_REF": "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=", + "ECK": "http://www.ecogene.org/geneInfo.php?eck_id=", + "CGD": "http://identifiers.org/cgd/", + "GR_GENE": "http://identifiers.org/gramene.gene/", + "RNAmods": "http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?", + "KEGG_ENZYME": "http://identifiers.org/kegg.enzyme/", + "CACAO": "http://gowiki.tamu.edu/wiki/index.php/", + "IUPHAR_GPCR": "http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=", + "JCVI_TIGRFAMS": "http://search.jcvi.org/search?p&q=", + "SOY_QTL": "http://soybase.org/sbt/search/search_results.php?category=QTLName&search_term=", + "DDBJ": "http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=", + "PRINTS": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=", + "PO_REF": "http://planteome.org/po_ref/", + "IMG": "http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=", + "CL": "http://purl.obolibrary.org/obo/CL_", + "UniProtKB-SubCell": "http://www.uniprot.org/locations/", + "NIF_Subcellular": "http://www.neurolex.org/wiki/", + "GeneDB": "http://identifiers.org/genedb/", + "ApiDB_PlasmoDB": "http://www.plasmodb.org/gene/", + "RNAcentral": "http://rnacentral.org/rna/", + "CGD_LOCUS": "http://www.candidagenome.org/cgi-bin/locus.pl?locus=", + "Rfam": "http://rfam.sanger.ac.uk/family/", + "Broad_NEUROSPORA": "http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S", + "AGI_LocusCode": "http://arabidopsis.org/servlets/TairObject?type=locus&name=", + "OBO_SF2_PO": "http://sourceforge.net/p/obo/plant-ontology-po-term-requests/", + "FMA": "http://purl.obolibrary.org/obo/FMA_", + "CDD": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=", + "PubChem_Compound": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=", + "HGNC_gene": "http://identifiers.org/hgnc.gene/", + "PharmGKB": "http://www.pharmgkb.org/do/serve?objId=", + "VMD": "http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=", + "UniParc": "http://www.uniprot.org/uniparc/", + "MEROPS": "http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=", + "GDB": "http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:", + "SEED": "http://www.theseed.org/linkin.cgi?id=", + "SO": "http://purl.obolibrary.org/obo/SO_", + "Soy_gene": "http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=", + "PECO_GIT": "https://github.com/Planteome/plant-environment-ontology/issues/", + "CORUM": "http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=", + "RHEA": "http://www.rhea-db.org/reaction.xhtml?id=", + "dbSNP": "http://identifiers.org/dbsnp/", + "MaizeGDB_Locus": "http://identifiers.org/maizegdb.locus/", + "MO": "http://mged.sourceforge.net/ontologies/MGEDontology.php#", + "PLANA_REF": "http://purl.obolibrary.org/obo/plana/references/", + "BRENDA": "http://purl.obolibrary.org/obo/BTO_", + "ASAP": "https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=", + "CAS": "http://identifiers.org/cas/", + "H-invDB_locus": "http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=", + "UM-BBD_ruleID": "http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=", + "taxon": "http://purl.obolibrary.org/obo/NCBITaxon_", + "ComplexPortal": "https://www.ebi.ac.uk/complexportal/complex/", + "JSTOR": "http://www.jstor.org/stable/", + "GRIMS": "https://www.genesys-pgr.org/acn/search2?q=IRGC+", + "PATO": "http://purl.obolibrary.org/obo/PATO_", + "GR_QTL": "http://identifiers.org/gramene.qtl/", + "ECOGENE": "http://www.ecogene.org/geneInfo.php?eg_id=", + "HPA_antibody": "http://www.proteinatlas.org/antibody_info.php?antibody_id=", + "VBRC": "http://vbrc.org/query.asp?web_id=VBRC:", + "EO_GIT": "https://github.com/Planteome/plant-environment-ontology/issues/", + "EchoBASE": "http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=", + "CASGEN": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=", + "IUPHAR_RECEPTOR": "http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=", + "IRIC": "http://oryzasnp.org/_variety.zul?irisid=", + "GenBank": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=", + "TGD": "http://identifiers.org/tgd/", + "JCVI_EGAD": "http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=", + "PubChem_BioAssay": "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=", + "TC": "http://www.tcdb.org/tcdb/index.php?tc=", + "SABIO-RK": "http://sabio.villa-bosch.de/reacdetails.jsp?reactid=", + "OBO_SF2_PECO": "https://sourceforge.net/p/obo/plant-environment-ontology-eo/", + "MetaCyc": "http://identifiers.org/metacyc/", + "PAMGO_GAT": "http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=", + "ModBase": "http://salilab.org/modbase/searchbyid?databaseID=", + "OMIM": "http://omim.org/entry/", + "GR_MUT": "http://www.gramene.org/db/genes/search_gene?acc=", + "HPA": "http://www.proteinatlas.org/tissue_profile.php?antibody_id=", + "IntAct": "http://identifiers.org/intact/", + "ProDom": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=", + "GRIN": "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=", + "WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_", + "BioCyc": "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=", + "ENSEMBL_GeneID": "http://www.ensembl.org/id/", + "PIR": "http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=", + "UniProtKB-KW": "http://www.uniprot.org/keywords/", + "Planteome_gene": "https://www.google.com/search?q=", + "AspGD": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=", + "JCVI_Medtr": "http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=", + "EuPathDB": "http://eupathdb.org/gene/", + "PMCID": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=" + } +} From 6997cc2864f87ac07173c97fbcdb3f94de33ad6f Mon Sep 17 00:00:00 2001 From: cmungall Date: Thu, 19 Apr 2018 14:45:09 -0700 Subject: [PATCH 2/4] Build go context from yaml https://github.com/geneontology/go-site/issues/617 --- Makefile | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 0da257b..d187a4c 100644 --- a/Makefile +++ b/Makefile @@ -76,6 +76,10 @@ COMMONS_SOURCES = semweb idot_nr monarch obo registry/commons_context.jsonld: $(patsubst %, registry/%_context.jsonld, $(COMMONS_SOURCES)) python3 ./bin/concat-context.py $^ > $@.tmp && mv $@.tmp $@ +GO_SOURCES = semweb goxrefs obo +registry/go_context.jsonld: $(patsubst %, registry/%_context.jsonld, $(COMMONS_SOURCES)) + python3 ./bin/concat-context.py $^ > $@.tmp && mv $@.tmp $@ + SUPERSET_SOURCES = goxrefs idot semweb monarch semweb_vocab ro_vocab obo reports/clashes.txt: $(patsubst %, registry/%_context.jsonld, $(SUPERSET_SOURCES)) (python3 ./bin/concat-context.py $^ > registry/superset.jsonld) >& $@ @@ -89,7 +93,10 @@ reports/clashes-$(A)-$(B)-$(C).txt: $(patsubst %, registry/%_context.jsonld, $(A (python3 ./bin/concat-context.py $^ > registry/superset.jsonld) >& $@ ## GO -registry/go-db-xrefs.json: ../go-site/metadata/db-xrefs.yaml +## TODO +registry/go-db-xrefs.yaml: + wget --no-check-certificate https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml -O $@ +registry/go-db-xrefs.json: registry/go-db-xrefs.yaml ./bin/yaml2json.pl $< > $@ From 5c150279550c7abd26e02b491f940b279b35c370 Mon Sep 17 00:00:00 2001 From: cmungall Date: Thu, 19 Apr 2018 14:47:35 -0700 Subject: [PATCH 3/4] clashes --- reports/clashes.txt | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/reports/clashes.txt b/reports/clashes.txt index a74d966..9312453 100644 --- a/reports/clashes.txt +++ b/reports/clashes.txt @@ -1,5 +1,5 @@ WARNING: clash for CL. Was=http://purl.obolibrary.org/obo/CL_ [registry/goxrefs_context.jsonld], Now=http://identifiers.org/cl/ [registry/idot_context.jsonld] -WARNING: clash for RGD. Was=http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword= [registry/goxrefs_context.jsonld], Now=http://identifiers.org/rgd/ [registry/idot_context.jsonld] +WARNING: clash for RGD. Was=http://rgd.mcw.edu/rgdweb/search/search.html?term= [registry/goxrefs_context.jsonld], Now=http://identifiers.org/rgd/ [registry/idot_context.jsonld] WARNING: clash for SMART. Was=http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN= [registry/goxrefs_context.jsonld], Now=http://identifiers.org/smart/ [registry/idot_context.jsonld] WARNING: clash for CDD. Was=http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid= [registry/goxrefs_context.jsonld], Now=http://identifiers.org/cdd/ [registry/idot_context.jsonld] WARNING: clash for ENSEMBL. Was=http://www.ensembl.org/id/ [registry/goxrefs_context.jsonld], Now=http://identifiers.org/ensembl/ [registry/idot_context.jsonld] @@ -78,20 +78,19 @@ WARNING: clash for PomBase. Was=http://www.pombase.org/spombe/result/ [registry/ WARNING: clash for RGD. Was=http://identifiers.org/rgd/ [registry/idot_context.jsonld], Now=http://rgd.mcw.edu/rgdweb/report/gene/main.html?id= [registry/monarch_context.jsonld] WARNING: clash for RO. Was=http://identifiers.org/ro/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/RO_ [registry/monarch_context.jsonld] WARNING: clash for RefSeq. Was=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val= [registry/goxrefs_context.jsonld], Now=http://www.ncbi.nlm.nih.gov/refseq/?term= [registry/monarch_context.jsonld] -WARNING: clash for SGD. Was=http://identifiers.org/sgd/ [registry/idot_context.jsonld], Now=http://identifiers.org/SGD: [registry/monarch_context.jsonld] WARNING: clash for SO. Was=http://identifiers.org/so/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/SO_ [registry/monarch_context.jsonld] WARNING: clash for TAIR. Was=http://arabidopsis.org/servlets/TairObject?type=communication&id= [registry/goxrefs_context.jsonld], Now=http://identifiers.org/TAIR: [registry/monarch_context.jsonld] WARNING: clash for UBERON. Was=http://identifiers.org/uberon/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/UBERON_ [registry/monarch_context.jsonld] -WARNING: clash for UMLS. Was=http://identifiers.org/umls/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/UMLS_ [registry/monarch_context.jsonld] +WARNING: clash for UMLS. Was=http://identifiers.org/umls/ [registry/idot_context.jsonld], Now=http://linkedlifedata.com/resource/umls/id/ [registry/monarch_context.jsonld] WARNING: clash for UNII. Was=http://identifiers.org/unii/ [registry/idot_context.jsonld], Now=http://fdasis.nlm.nih.gov/srs/unii/ [registry/monarch_context.jsonld] WARNING: clash for UO. Was=http://identifiers.org/uo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/UO_ [registry/monarch_context.jsonld] WARNING: clash for UniProtKB. Was=http://www.uniprot.org/uniprot/ [registry/goxrefs_context.jsonld], Now=http://identifiers.org/uniprot/ [registry/monarch_context.jsonld] WARNING: clash for WBPhenotype. Was=http://www.wormbase.org/species/c_elegans/phenotype/WBPhenotype: [registry/goxrefs_context.jsonld], Now=http://purl.obolibrary.org/obo/WBPhenotype_ [registry/monarch_context.jsonld] +WARNING: clash for Xenbase. Was=http://www.xenbase.org/common/xsearch.do?searchValue= [registry/goxrefs_context.jsonld], Now=http://identifiers.org/xenbase/ [registry/monarch_context.jsonld] WARNING: clash for ZFIN. Was=http://identifiers.org/zfin/ [registry/idot_context.jsonld], Now=http://zfin.org/ [registry/monarch_context.jsonld] WARNING: clash for dc. Was=http://purl.org/dc/terms/ [registry/semweb_context.jsonld], Now=http://purl.org/dc/elements/1.1/ [registry/monarch_context.jsonld] WARNING: clash for 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: clash for BTO. Was=http://identifiers.org/bto/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/BTO_ [registry/obo_context.jsonld] -WARNING: clash for EO. Was=http://identifiers.org/eo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/EO_ [registry/obo_context.jsonld] WARNING: clash for FMA. Was=http://identifiers.org/fma/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/FMA_ [registry/obo_context.jsonld] WARNING: clash for GEO. Was=http://identifiers.org/geo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/GEO_ [registry/obo_context.jsonld] WARNING: clash for MAMO. Was=http://identifiers.org/mamo/ [registry/idot_context.jsonld], Now=http://purl.obolibrary.org/obo/MAMO_ [registry/obo_context.jsonld] From 0744c4e62004147fe673e99f61ad840f0067ebde Mon Sep 17 00:00:00 2001 From: cmungall Date: Thu, 19 Apr 2018 14:55:04 -0700 Subject: [PATCH 4/4] rename --- Makefile | 8 +- registry/go-db-xrefs.json | 5268 ----------------- ...xrefs_context.jsonld => go_context.jsonld} | 0 registry/monarch_context.jsonld | 4 +- registry/obo_context.jsonld | 1 - 5 files changed, 6 insertions(+), 5275 deletions(-) delete mode 100644 registry/go-db-xrefs.json rename registry/{goxrefs_context.jsonld => go_context.jsonld} (100%) diff --git a/Makefile b/Makefile index d187a4c..827eda9 100644 --- a/Makefile +++ b/Makefile @@ -1,6 +1,6 @@ # Makefile to generate source JSON-LD contexts plus merged contexts -CONTEXTS := pr goxrefs obo idot idot_nr semweb monarch semweb_vocab ro_vocab commons +CONTEXTS := pr go obo idot idot_nr semweb monarch semweb_vocab ro_vocab commons all: $(patsubst %,registry/%_context.jsonld,$(CONTEXTS)) reports/clashes.txt @@ -28,7 +28,7 @@ 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/goxrefs_context.jsonld: registry/go-db-xrefs.json +registry/go_context.jsonld: registry/go-db-xrefs.json ./bin/go-xrefs-to-context.py $< > $@.tmp && mv $@.tmp $@ ## Monarch @@ -76,11 +76,11 @@ COMMONS_SOURCES = semweb idot_nr monarch obo registry/commons_context.jsonld: $(patsubst %, registry/%_context.jsonld, $(COMMONS_SOURCES)) python3 ./bin/concat-context.py $^ > $@.tmp && mv $@.tmp $@ -GO_SOURCES = semweb goxrefs obo +GO_SOURCES = semweb go obo registry/go_context.jsonld: $(patsubst %, registry/%_context.jsonld, $(COMMONS_SOURCES)) python3 ./bin/concat-context.py $^ > $@.tmp && mv $@.tmp $@ -SUPERSET_SOURCES = goxrefs idot semweb monarch semweb_vocab ro_vocab obo +SUPERSET_SOURCES = go idot semweb monarch semweb_vocab ro_vocab obo reports/clashes.txt: $(patsubst %, registry/%_context.jsonld, $(SUPERSET_SOURCES)) (python3 ./bin/concat-context.py $^ > registry/superset.jsonld) >& $@ diff --git a/registry/go-db-xrefs.json b/registry/go-db-xrefs.json deleted file mode 100644 index cefb213..0000000 --- a/registry/go-db-xrefs.json +++ /dev/null @@ -1,5268 +0,0 @@ -[ - { - "generic_urls" : [ - "http://www.agbase.msstate.edu/" - ], - "name" : "AgBase resource for functional analysis of agricultural plant and animal gene products", - "entity_types" : [ - { - "type_id" : "BET:0000000", - "url_syntax" : "http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=[example_id]", - "type_name" : "entity" - } - ], - "database" : "AgBase" - }, - { - "description" : "Comprises TAIR, TIGR and MIPS", - "name" : "Arabidopsis Genome Initiative", - "database" : "AGI_LocusCode", - "entity_types" : [ - { - "type_id" : "SO:0000704", - "url_syntax" : "http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]", - "id_syntax" : "A[Tt][MmCc0-5][Gg][0-9]{5}(\\.[0-9]{1})?", - "example_id" : "AGI_LocusCode:At2g17950", - "type_name" : "gene", - "example_url" : "http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950" - } - ], - "generic_urls" : [ - "http://www.arabidopsis.org" - ] - }, - { - "generic_urls" : [ - "http://agricola.nal.usda.gov/" - ], - "name" : "AGRICultural OnLine Access", - "database" : "AGRICOLA_ID", - "entity_types" : [ - { - "type_name" : "entity", - "type_id" : "BET:0000000", - "example_id" : "AGRICOLA_NAL:TP248.2 P76 v.14" - } - ] - }, - { - "generic_urls" : [ - "http://agricola.nal.usda.gov/" - ], - "database" : "AGRICOLA_IND", - "entity_types" : [ - { - "type_name" : "entity", - "example_id" : "AGRICOLA_IND:IND23252955", - "type_id" : "BET:0000000" - } - ], - "name" : "AGRICultural OnLine Access" - }, - { - "generic_urls" : [ - "http://www.ims.utoronto.ca/" - ], - "database" : "Alzheimers_University_of_Toronto", - "entity_types" : [ - { - "type_id" : "BET:0000000", - "type_name" : "entity" - } - ], - "name" : "Alzheimers Project at University of Toronto" - }, - { - "entity_types" : [ - { - "example_url" : "http://www.plasmodb.org/gene/PF11_0344", - "type_name" : "entity", - "example_id" : "ApiDB_PlasmoDB:PF11_0344", - "type_id" : "BET:0000000", - "url_syntax" : "http://www.plasmodb.org/gene/[example_id]" - } - ], - "database" : "ApiDB_PlasmoDB", - "name" : "PlasmoDB Plasmodium Genome Resource", - "generic_urls" : [ - "http://plasmodb.org/" - ] - }, - { - "generic_urls" : [ - "http://www.mobot.org/mobot/research/apweb/" - ], - "entity_types" : [ - { - "url_syntax" : "http://www.apsnet.org/publications/commonnames/Pages/[example_id].aspx", - "type_id" : "BET:0000000", - "example_id" : "APSNET:AfricanDaisy", - "type_name" : "entity", - "example_url" : "http://www.apsnet.org/publications/commonnames/Pages/AfricanDaisy.aspx" - } - ], - "database" : "APSNET", - "name" : "APSNET Common Names of Plant Diseases" - }, - { - "name" : "Angiosperm Phylogeny Website", - "database" : "APweb", - "entity_types" : [ - { - "type_id" : "BET:0000000", - "url_syntax" : "http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html", - "example_id" : "APweb:Glossary", - "type_name" : "entity", - "example_url" : "http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html" - } - ], - "generic_urls" : [ - "http://www.mobot.org/mobot/research/apweb/" - ] - }, - { - "generic_urls" : [ - "http://www.arabidopsis.org/biocyc/index.jsp" - ], - "entity_types" : [ - { - "example_url" : "http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=PWYQT-62", - "type_name" : "entity", - "example_id" : "AraCyc:PWYQT-62", - "url_syntax" : "http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=[example_id]", - "type_id" : "BET:0000000" - } - ], - "database" : "AraCyc", - "name" : "AraCyc metabolic pathway database for Arabidopsis thaliana" - }, - { - "name" : "Alzheimers Research Gene Ontology Initiative", - "entity_types" : [ - { - "type_name" : "entity", - "type_id" : "BET:0000000" - } - ], - "database" : "ARUK-UCL", - "generic_urls" : [ - "http://www.ucl.ac.uk/functional-gene-annotation/neurological" - ] - }, - { - "generic_urls" : [ - "https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm" - ], - "name" : "A Systematic Annotation Package for Community Analysis of Genomes", - "database" : "ASAP", - "entity_types" : [ - { - "type_id" : "SO:0000704", - "url_syntax" : "https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=[example_id]", - "example_id" : "ASAP:ABE-0000008", - "type_name" : "gene", - "example_url" : "https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=ABE-0000008" - } - ] - }, - { - "generic_urls" : [ - "http://www.aspergillusgenome.org/" - ], - "entity_types" : [ - { - "id_syntax" : "ASPL[0-9]{10}", - "example_id" : "AspGD:ASPL0000067538", - "type_id" : "SO:0000704", - "url_syntax" : "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=[example_id]", - "example_url" : "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=ASPL0000067538", - "type_name" : "gene" - } - ], - "database" : "AspGD", - "synonyms" : [ - "ASPGD", - "AspGDID" - ], - "name" : "Aspergillus Genome Database" - }, - { - "generic_urls" : [ - "http://www.aspergillusgenome.org/" - ], - "entity_types" : [ - { - "example_url" : "http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN10942", - "type_name" : "entity", - "example_id" : "AspGD_LOCUS:AN10942", - "type_id" : "BET:0000000", - "url_syntax" : "http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=[example_id]" - } - ], - "database" : "AspGD_LOCUS", - "name" : "Aspergillus Genome Database" - }, - { - "entity_types" : [ - { - "type_name" : "entity", - "example_url" : "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=90", - "url_syntax" : "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]", - "type_id" : "BET:0000000", - "example_id" : "AspGD_REF:90" - } - ], - "database" : "AspGD_REF", - "name" : "Aspergillus Genome Database", - "generic_urls" : [ - "http://www.aspergillusgenome.org/" - ] - }, - { - "generic_urls" : [ - "http://purl.obolibrary.org/obo/bfo" - ], - "entity_types" : [ - { - "example_id" : "BFO:0000066", - "url_syntax" : "http://purl.obolibrary.org/obo/BFO_[example_id]", - "type_id" : "BET:0000000", - "example_url" : "http://purl.obolibrary.org/obo/BFO_0000066", - "type_name" : "entity" - } - ], - "database" : "BFO", - "name" : "Basic Formal Ontology", - "description" : "An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050)" - }, - { - "generic_urls" : [ - "http://www.ucl.ac.uk/cardiovasculargeneontology/" - ], - "entity_types" : [ - { - "type_id" : "BET:0000000", - "type_name" : "entity" - } - ], - "database" : "BHF-UCL", - "name" : "Cardiovascular Gene Ontology Annotation Initiative", - "description" : "The Cardiovascular Gene Ontology Annotation Initiative is supported by the British Heart Foundation (BHF) and located at University College London (UCL)." - }, - { - "name" : "BioCyc collection of metabolic pathway databases", - "database" : "BioCyc", - "entity_types" : [ - { - "example_url" : "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271", - "type_name" : "entity", - "example_id" : "BioCyc:PWY-5271", - "url_syntax" : "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id]", - "type_id" : "BET:0000000" - } - ], - "generic_urls" : [ - "http://biocyc.org/" - ] - }, - { - "entity_types" : [ - { - "example_url" : "http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=BIOMD0000000045", - "type_name" : "entity", - "example_id" : "BIOMD:BIOMD0000000045", - "type_id" : "BET:0000000", - "url_syntax" : "http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=[example_id]" - } - ], - "database" : "BIOMD", - "name" : "BioModels Database", - "synonyms" : [ - "BIOMDID" - ], - "generic_urls" : [ - "http://www.ebi.ac.uk/biomodels/" - ] - }, - { - "entity_types" : [ - { - "type_name" : "entity", - "type_id" : "BET:0000000" - } - ], - "database" : "bioPIXIE_MEFIT", - "name" : "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology", - "generic_urls" : [ - "http://avis.princeton.edu/mefit/", - "http://pixie.princeton.edu/pixie/" - ] - }, - { - "generic_urls" : [ - "http://www.biosis.org/" - ], - "name" : "BIOSIS previews", - "database" : "BIOSIS", - "entity_types" : [ - { - "type_id" : "BET:0000000", - "example_id" : "BIOSIS:200200247281", - "type_name" : "entity" - } - ] - }, - { - "generic_urls" : [ - "http://www.brenda-enzymes.info" - ], - "entity_types" : [ - { - "example_id" : "BRENDA:4.2.1.3", - "type_id" : "GO:0003824", - "url_syntax" : "http://www.brenda-enzymes.info/php/result_flat.php4?ecno=[example_id]", - "example_url" : "http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3", - "type_name" : "catalytic activity" - } - ], - "database" : "BRENDA", - "name" : "BRENDA, The Comprehensive Enzyme Information System" - }, - { - "database" : "Broad", - "entity_types" : [ - { - "type_id" : "BET:0000000", - "type_name" : "entity" - } - ], - "name" : "Broad Institute", - "generic_urls" : [ - "http://www.broad.mit.edu/" - ] - }, - { - "description" : "Magnaporthe grisea Database at the Broad Institute", - "name" : "Magnaporthe grisea Database", - "entity_types" : [ - { - "example_id" : "Broad_MGG:MGG_05132.5", - "type_id" : "BET:0000000", - "url_syntax" : "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S[example_id]", - "example_url" : "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=SMGG_05132", - "type_name" : "entity" - } - ], - "database" : "Broad_MGG", - "generic_urls" : [ - "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html" - ] - }, - { - "generic_urls" : [ - "http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html" - ], - "name" : "Neurospora crassa Database", - "description" : "Neurospora crassa database at the Broad Institute", - "entity_types" : [ - { - "example_id" : "BROAD_NEUROSPORA:7000007580576824", - "type_id" : "BET:0000000", - "url_syntax" : "http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S[example_id]", - "example_url" : "http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000007580576824", - "type_name" : "entity" - } - ], - "database" : "Broad_NEUROSPORA" - }, - { - "description" : "The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.", - "name" : "Community Assessment of Community Annotation with Ontologies", - "entity_types" : [ - { - "url_syntax" : "http://gowiki.tamu.edu/wiki/index.php/[example_id]", - "type_id" : "BET:0000000", - "example_id" : "MYCS2:A0QNF5", - "type_name" : "entity", - "example_url" : "http://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5" - } - ], - "database" : "CACAO", - "generic_urls" : [ - "http://gowiki.tamu.edu/wiki/index.php/Category:CACAO" - ] - }, - { - "generic_urls" : [ - "http://biofunctionprediction.org/cafa/" - ], - "name" : "Critical Assessment of Protein Function Annotation", - "entity_types" : [ - { - "type_name" : "entity", - "type_id" : "BET:0000000" - } - ], - "database" : "CAFA" - }, - { - "entity_types" : [ - { - "type_id" : "BET:0000000", - "example_id" : "CAS:58-08-2", - "type_name" : "entity" - } - ], - "database" : "CAS", - "name" : "CAS Chemical Registry", - "description" : "CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s.", - "generic_urls" : [ - "http://www.cas.org/expertise/cascontent/registry/index.html" - ] - }, - { - "generic_urls" : [ - "http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html" - ], - "database" : "CASGEN", - "entity_types" : [ - { - "example_id" : "CASGEN:1040", - "type_id" : "BET:0000000", - "url_syntax" : "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=[example_id]", - "example_url" : "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=1040", - "type_name" : "entity" - } - ], - "name" : "Catalog of Fishes genus database", - "synonyms" : [ - "CAS_GEN" - ] - }, - { - "database" : "CASREF", - "entity_types" : [ - { - "type_id" : "BET:0000000", - "url_syntax" : "http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id]", - 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} - ], - "name" : "Zebrafish Information Network" - }, - { - "generic_urls" : [ - "http://purl.obolibrary.org/obo/plana/references/" - ], - "database" : "PLANA_REF", - "entity_types" : [ - { - "type_name" : "entity", - "example_url" : "http://purl.obolibrary.org/obo/plana/references/0000001", - "type_id" : "BET:0000000", - "url_syntax" : "http://purl.obolibrary.org/obo/plana/references/[example_id]", - "id_syntax" : "\\d{7}", - "example_id" : "0000001" - } - ], - "name" : "Planaria Ontology Database References" - } -] diff --git a/registry/goxrefs_context.jsonld b/registry/go_context.jsonld similarity index 100% rename from registry/goxrefs_context.jsonld rename to registry/go_context.jsonld diff --git a/registry/monarch_context.jsonld b/registry/monarch_context.jsonld index 8548c0f..e8f2a5c 100644 --- a/registry/monarch_context.jsonld +++ b/registry/monarch_context.jsonld @@ -128,7 +128,7 @@ "RXCUI": "http://purl.bioontology.org/ontology/RXNORM/", "RefSeq": "http://www.ncbi.nlm.nih.gov/refseq/?term=", "SEPIO": "http://purl.obolibrary.org/obo/SEPIO_", - "SGD": "http://identifiers.org/SGD:", + "SGD": "http://identifiers.org/sgd/", "SGD_REF": "https://www.yeastgenome.org/reference/", "SIO": "http://semanticscience.org/resource/SIO_", "SNOMED": "http://purl.obolibrary.org/obo/SNOMED_", @@ -139,7 +139,7 @@ "TrEMBL": "http://www.uniprot.org/uniprot/", "UBERON": "http://purl.obolibrary.org/obo/UBERON_", "UCSC": "ftp://hgdownload.cse.ucsc.edu/goldenPath/", - "UMLS": "http://purl.obolibrary.org/obo/UMLS_", + "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_", diff --git a/registry/obo_context.jsonld b/registry/obo_context.jsonld index 4dcab08..e97c809 100644 --- a/registry/obo_context.jsonld +++ b/registry/obo_context.jsonld @@ -35,7 +35,6 @@ "EHDAA2": "http://purl.obolibrary.org/obo/EHDAA2_", "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_",