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Updated BridgeDb Datasources from bridgedb/datasources#43
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egonw committed Aug 26, 2023
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4 changes: 2 additions & 2 deletions org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
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Expand Up @@ -123,7 +123,7 @@ SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/prote
SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki subtiwiki gene
SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM supfam protein
SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids swisslipid metabolite
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite
Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology
TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene
TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene
Expand All @@ -133,7 +133,7 @@ TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch
UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser P2576 ucsc gene
UMLS CUI Cu https://www.nlm.nih.gov/research/umls/rxnorm/index.html https://www.ncbi.nlm.nih.gov/medgen/{$id} 760050 other Homo sapiens 1 urn:miriam:medgen ^[CN]*\d{4,7}$ MedGen medgen other
Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 ^UPA\d{5}$ Unipathway upa pathway
Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein
UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein
VMH metabolite VmhM http://www.vmh.life https://www.vmh.life/#metabolite/$id h2o metabolite 1 [a-zA-Z0-9_\(\_\)\[\]]+ VMH Life_Metabolite vmhmetabolite metabolite
Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 1-FEH+w3 gene Triticum aestivum 1 Wn Wheat gene names graingenes.symbol gene
Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs graingenes.reference gene
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4 changes: 2 additions & 2 deletions org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/prote
SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki subtiwiki gene
SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM supfam protein
SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids swisslipid metabolite
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite
Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology
TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene
TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene
Expand All @@ -133,7 +133,7 @@ TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch
UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser P2576 ucsc gene
UMLS CUI Cu https://www.nlm.nih.gov/research/umls/rxnorm/index.html https://www.ncbi.nlm.nih.gov/medgen/{$id} 760050 other Homo sapiens 1 urn:miriam:medgen ^[CN]*\d{4,7}$ MedGen medgen other
Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 ^UPA\d{5}$ Unipathway upa pathway
Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein
UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein
VMH metabolite VmhM http://www.vmh.life https://www.vmh.life/#metabolite/$id h2o metabolite 1 [a-zA-Z0-9_\(\_\)\[\]]+ VMH Life_Metabolite vmhmetabolite metabolite
Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 1-FEH+w3 gene Triticum aestivum 1 Wn Wheat gene names graingenes.symbol gene
Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs graingenes.reference gene
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