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Updated the BridgeDb Datasources 20250728
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‎org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv‎

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -23,23 +23,22 @@ dbSNP Sn http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp http://www.ncbi.nlm.nih
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DrugBank Dr http://www.drugbank.ca/ http://www.drugbank.ca/drugs/$id DB00001 metabolite 1 urn:miriam:drugbank ^D(B|BSALT|BCAT)(\d{1})?\d{5}$ DrugBank P715 drugbank metabolite
2424
DOI Pbd https://doi.org/ https://doi.org/$id 10.1038/s41597-020-0477-8 publication 1 urn:miriam:doi ^\d{2}\.\d{4}.*$ Digital Object Identifier P356 doi publication
2525
EcoCyc Eco http://ecocyc.org/ http://ecocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=$id 1.1.1.127-RXN interaction Escherichia coli 1 Eco ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+-RXN EcoCyc ecocyc interaction
26-
EcoGene Ec http://ecogene.org/ http://ecogene.org/geneInfo.php?eg_id=$id EG10173 gene Escherichia coli 1 urn:miriam:ecogene ^EG\d+$ EcoGene ecogene gene
2726
EMBL Em http://www.ebi.ac.uk/embl/ http://www.ebi.ac.uk/ena/data/view/$id X58356 gene 1 urn:miriam:ena.embl ^[A-Z]+[0-9]+$ European Nucleotide Archive ena.embl gene
2827
Ensembl En http://www.ensembl.org/ https://www.ensembl.org/id/$id ENSG00000139618 gene 1 urn:miriam:ensembl ^ENS[A-Z]*[FPTG]\d{11}$ Ensembl P594 ensembl gene
2928
Entrez Gene L http://www.ncbi.nlm.nih.gov/gene http://www.ncbi.nlm.nih.gov/gene/$id 100010 gene 1 urn:miriam:ncbigene ^\d+$ Entrez Gene P351 ncbigene gene
30-
Enzyme Nomenclature E http://www.ebi.ac.uk/intenz/ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 gene 1 urn:miriam:ec-code ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ Enzyme Nomenclature P591 eccode gene
29+
Enzyme Nomenclature E http://www.ebi.ac.uk/intenz/ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 gene 1 urn:miriam:ec-code ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ Enzyme Nomenclature P591 ec gene
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EPA CompTox Ect https://comptox.epa.gov/dashboard https://comptox.epa.gov/dashboard/$id DTXSID7020637 metabolite 1 Ect ^DTXSID(\d{2})?\d{7}\d?$ EPA CompTox Dashboard P3117 comptox metabolite
3231
European Registry of Materials Nmerm https://nanocommons.github.io/identifiers/ ERM00000064 material 0 ^ERM\d{8}$ European Registry of Materials erm material
3332
FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 gene Drosophila melanogaster 1 urn:miriam:fb ^FB\w{2}\d{7}$ FlyBase P3852 flybase gene
3433
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene
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Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene
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GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology
37-
Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
36+
Gramene Arabidopsis EnAt https://www.gramene.org/ https://plants.ensembl.org/id/$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis ensembl.plant gene
3837
Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
3938
Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
40-
Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
39+
Gramene Maize EnZm https://www.ensembl.org https://plants.ensembl.org/id/$id GRMZM2G174107 gene 1 EnZm ^GRMZM2G\d+$ Gramene Maize ensembl.plant gene
4140
Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
42-
Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
41+
Gramene Rice EnOj https://www.gramene.org/ https://plants.ensembl.org/id/$id Os05g0113900 gene 1 EnOj ^Os\d.*$ Gramene Rice ensembl.plant gene
4342
Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene
4443
Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite
4544
HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
@@ -70,7 +69,7 @@ LIPID MAPS Lm http://www.lipidmaps.org https://www.lipidmaps.org/data/structure/
7069
LipidBank Lb http://lipidbank.jp/index.html http://lipidbank.jp/cgi-bin/detail.cgi?id=$id BBA0001 metabolite 1 urn:miriam:lipidbank ^\w+\d+$ LipidBank lipidbank metabolite
7170
MACiE Ma http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id M0001 protein 1 urn:miriam:macie ^M\d{4}$ MACiE macie protein
7271
MaizeGDB Mg https://maizegdb.org/ https://maizegdb.org/gene_center/gene/$id acc1 gene Zea mays 1 Mg MaizeGDB maizegdb.locus gene
73-
MatrixDB Md http://matrixdb.ibcp.fr/ http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association P00747_P07355 interaction 1 urn:miriam:matrixdb.association ^([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]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ MatrixDB matrixdb.association interaction
72+
MatrixDB Md http://matrixdb.univ-lyon1.fr/ http://matrixdb.univ-lyon1.fr/association/$id P00747_P07355 interaction 1 urn:miriam:matrixdb.association ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ MatrixDB matrixdb.association interaction
7473
MeSH Me http://id.nlm.nih.gov/mesh/ http://id.nlm.nih.gov/mesh/$id C000100 other 1 urn:miriam:mesh ^(C|D)\d{6}$ Medical Subject Headings mesh disease,metabolite,gene,other
7574
MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.uk/metabolights/$id MTBLC17170 metabolite 1 Ml ^MTBLC\d{1,6}$ MetaboLights Compounds P3890 metabolights metabolite
7675
MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction
@@ -111,7 +110,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
111110
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
112111
RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene
113112
Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction
114-
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
113+
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://plants.ensembl.org/id/$id Os04g54800 gene Oryza sativa 1 Os ^Os.*$ Rice Ensembl Gene ensembl.plant gene
115114
SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene
116115
Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway
117116
SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein

‎org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv‎

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -23,23 +23,22 @@ dbSNP Sn http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp http://www.ncbi.nlm.nih
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DrugBank Dr http://www.drugbank.ca/ http://www.drugbank.ca/drugs/$id DB00001 metabolite 1 urn:miriam:drugbank ^D(B|BSALT|BCAT)(\d{1})?\d{5}$ DrugBank P715 drugbank metabolite
2424
DOI Pbd https://doi.org/ https://doi.org/$id 10.1038/s41597-020-0477-8 publication 1 urn:miriam:doi ^\d{2}\.\d{4}.*$ Digital Object Identifier P356 doi publication
2525
EcoCyc Eco http://ecocyc.org/ http://ecocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=$id 1.1.1.127-RXN interaction Escherichia coli 1 Eco ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+-RXN EcoCyc ecocyc interaction
26-
EcoGene Ec http://ecogene.org/ http://ecogene.org/geneInfo.php?eg_id=$id EG10173 gene Escherichia coli 1 urn:miriam:ecogene ^EG\d+$ EcoGene ecogene gene
2726
EMBL Em http://www.ebi.ac.uk/embl/ http://www.ebi.ac.uk/ena/data/view/$id X58356 gene 1 urn:miriam:ena.embl ^[A-Z]+[0-9]+$ European Nucleotide Archive ena.embl gene
2827
Ensembl En http://www.ensembl.org/ https://www.ensembl.org/id/$id ENSG00000139618 gene 1 urn:miriam:ensembl ^ENS[A-Z]*[FPTG]\d{11}$ Ensembl P594 ensembl gene
2928
Entrez Gene L http://www.ncbi.nlm.nih.gov/gene http://www.ncbi.nlm.nih.gov/gene/$id 100010 gene 1 urn:miriam:ncbigene ^\d+$ Entrez Gene P351 ncbigene gene
30-
Enzyme Nomenclature E http://www.ebi.ac.uk/intenz/ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 gene 1 urn:miriam:ec-code ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ Enzyme Nomenclature P591 eccode gene
29+
Enzyme Nomenclature E http://www.ebi.ac.uk/intenz/ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 gene 1 urn:miriam:ec-code ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ Enzyme Nomenclature P591 ec gene
3130
EPA CompTox Ect https://comptox.epa.gov/dashboard https://comptox.epa.gov/dashboard/$id DTXSID7020637 metabolite 1 Ect ^DTXSID(\d{2})?\d{7}\d?$ EPA CompTox Dashboard P3117 comptox metabolite
3231
European Registry of Materials Nmerm https://nanocommons.github.io/identifiers/ ERM00000064 material 0 ^ERM\d{8}$ European Registry of Materials erm material
3332
FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 gene Drosophila melanogaster 1 urn:miriam:fb ^FB\w{2}\d{7}$ FlyBase P3852 flybase gene
3433
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene
3534
Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene
3635
GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology
37-
Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
36+
Gramene Arabidopsis EnAt https://www.gramene.org/ https://plants.ensembl.org/id/$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis ensembl.plant gene
3837
Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
3938
Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
40-
Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
39+
Gramene Maize EnZm https://www.ensembl.org https://plants.ensembl.org/id/$id GRMZM2G174107 gene 1 EnZm ^GRMZM2G\d+$ Gramene Maize ensembl.plant gene
4140
Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
42-
Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
41+
Gramene Rice EnOj https://www.gramene.org/ https://plants.ensembl.org/id/$id Os05g0113900 gene 1 EnOj ^Os\d.*$ Gramene Rice ensembl.plant gene
4342
Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene
4443
Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite
4544
HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
@@ -70,7 +69,7 @@ LIPID MAPS Lm http://www.lipidmaps.org https://www.lipidmaps.org/data/structure/
7069
LipidBank Lb http://lipidbank.jp/index.html http://lipidbank.jp/cgi-bin/detail.cgi?id=$id BBA0001 metabolite 1 urn:miriam:lipidbank ^\w+\d+$ LipidBank lipidbank metabolite
7170
MACiE Ma http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id M0001 protein 1 urn:miriam:macie ^M\d{4}$ MACiE macie protein
7271
MaizeGDB Mg https://maizegdb.org/ https://maizegdb.org/gene_center/gene/$id acc1 gene Zea mays 1 Mg MaizeGDB maizegdb.locus gene
73-
MatrixDB Md http://matrixdb.ibcp.fr/ http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association P00747_P07355 interaction 1 urn:miriam:matrixdb.association ^([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]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ MatrixDB matrixdb.association interaction
72+
MatrixDB Md http://matrixdb.univ-lyon1.fr/ http://matrixdb.univ-lyon1.fr/association/$id P00747_P07355 interaction 1 urn:miriam:matrixdb.association ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ MatrixDB matrixdb.association interaction
7473
MeSH Me http://id.nlm.nih.gov/mesh/ http://id.nlm.nih.gov/mesh/$id C000100 other 1 urn:miriam:mesh ^(C|D)\d{6}$ Medical Subject Headings mesh disease,metabolite,gene,other
7574
MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.uk/metabolights/$id MTBLC17170 metabolite 1 Ml ^MTBLC\d{1,6}$ MetaboLights Compounds P3890 metabolights metabolite
7675
MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction
@@ -111,7 +110,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
111110
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
112111
RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene
113112
Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction
114-
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
113+
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://plants.ensembl.org/id/$id Os04g54800 gene Oryza sativa 1 Os ^Os.*$ Rice Ensembl Gene ensembl.plant gene
115114
SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene
116115
Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway
117116
SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein

‎org.bridgedb.rdf/resources/BioDataSource.ttl‎

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Original file line numberDiff line numberDiff line change
@@ -171,17 +171,6 @@ bridgeDB:DataSource_EcoCyc a bridgeDB:DataSource ;
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bridgeDB:Organism bridgeDB:Organism_Ec ;
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dcterms:alternative "EcoCyc" .
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174-
bridgeDB:DataSource_EcoGene a bridgeDB:DataSource ;
175-
bridgeDB:fullName "EcoGene" ;
176-
bridgeDB:systemCode "Ec" ;
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bridgeDB:mainUrl "http://ecogene.org/" ;
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bridgeDB:idExample "EG10173" ;
179-
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;
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bridgeDB:Organism bridgeDB:Organism_Ec ;
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bridgeDB:hasRegexPattern "^EG\\d+$" ;
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dcterms:alternative "EcoGene" .
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bridgeDB:DataSource_EMBL a bridgeDB:DataSource ;
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bridgeDB:fullName "EMBL" ;
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bridgeDB:systemCode "Em" ;

‎org.bridgedb.rdf/resources/DataSource.ttl‎

Lines changed: 4 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -397,13 +397,6 @@ bridgeDB:DataSource_drugbankEnzyme a bridgeDB:DataSource ;
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bridgeDB:type "unknown" ;
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bridgeDB:hasPrimaryUriPattern <http://www4.wiwiss.fu-berlin.de/drugbank/resource/enzymes/$id> .
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400-
bridgeDB:DataSource_EcoGene a bridgeDB:DataSource ;
401-
bridgeDB:fullName "EcoGene" ;
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bridgeDB:systemCode "Ec" ;
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bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;
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bridgeDB:Organism bridgeDB:Organism_Ec .
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bridgeDB:DataSource_EMBL a bridgeDB:DataSource ;
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bridgeDB:fullName "EMBL" ;
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bridgeDB:systemCode "Em" ;
@@ -523,7 +516,7 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
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bridgeDB:idExample "ATMG01360-TAIR-G" ;
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bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
525518
bridgeDB:type "gene" ;
526-
bridgeDB:hasPrimaryUriPattern <https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id> ;
519+
bridgeDB:hasPrimaryUriPattern <https://plants.ensembl.org/id/$id> ;
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bridgeDB:Organism bridgeDB:Organism_At .
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529522
bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
@@ -552,7 +545,7 @@ bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
552545
bridgeDB:idExample "GRMZM2G174107" ;
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bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;
555-
bridgeDB:hasPrimaryUriPattern <https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id> .
548+
bridgeDB:hasPrimaryUriPattern <https://plants.ensembl.org/id/$id> .
556549

557550
bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
558551
bridgeDB:fullName "Gramene Pathway" ;
@@ -569,7 +562,7 @@ bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ;
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bridgeDB:idExample "osa-MIR171a" ;
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bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;
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bridgeDB:hasPrimaryUriPattern <http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id> .
565+
bridgeDB:hasPrimaryUriPattern <https://plants.ensembl.org/id/$id> .
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bridgeDB:DataSource_HGNC a bridgeDB:DataSource ;
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bridgeDB:fullName "HGNC" ;
@@ -1054,7 +1047,7 @@ bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ;
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bridgeDB:idExample "LOC_Os04g54800" ;
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bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;
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bridgeDB:hasPrimaryUriPattern <https://www.gramene.org/Oryza_sativa/geneview?gene=$id> ;
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bridgeDB:hasPrimaryUriPattern <https://plants.ensembl.org/id/$id> ;
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bridgeDB:Organism bridgeDB:Organism_Os ;
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bridgeDB:hasRegexUriPattern <http://bio2rdf.org/ensembl:$id> .
10601053

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