- Timestamp:
- 01/08/12 20:09:00 (5 months ago)
- Location:
- trunk/org.bridgedb.bio
- Files:
-
- 2 modified
-
resources/org/bridgedb/bio/datasources.txt (modified) (9 diffs)
-
src/org/bridgedb/bio/BioDataSource.java (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
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trunk/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.txt
r549 r560 1 2D-PAGE protein http://2dbase.techfak.uni-bielefeld.de/ http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?ac=$id P39172 1 urn:miriam:2d-page.protein ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ 2D-PAGE protein 1 2 3DMET http://www.3dmet.dna.affrc.go.jp/ http://www.3dmet.dna.affrc.go.jp/html/$id.html B00162 metabolite 1 urn:miriam:3dmet ^B\d{5}$ 3DMET 2 3 Aclame http://aclame.ulb.ac.be/ http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$id mge:2 gene 1 urn:miriam:aclame ^mge:\d+$ Aclame 3 4 Affy X http://www.affymetrix.com/ http://www.ensembl.org/common/Lucene/Results?species=all;feature=OligoProbe;q=$id 1851_s_at probe 0 X .+_at 5 AGD http://agd.vital-it.ch/ http://agd.vital-it.ch/Ashbya_gossypii/geneview?gene=$id AGR144C 1 urn:miriam:agd ^ARG\w+$ AGD 4 6 Agilent Ag A_24_P98555 probe 0 Ag A_\d+_.+ 5 Anatomical Therapeutic Chemical http://www.whocc.no/atc_ddd_index/ http://www.whocc.no/atc_ddd_index/?code=$id A10BA02 metabolite 1 urn:miriam:atc ^(\w+(\-\w+)?(\.\w+)?/)?\d{4,7}(\.\d{4}(v\d+)?)?$ Anatomical Therapeutic Chemical 7 AmoebaDB http://amoebadb.org/amoeba/ http://amoebadb.org/amoeba/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id EDI_244000 1 urn:miriam:amoebadb ^EDI_\d+$ AmoebaDB 8 Anatomical Therapeutic Chemical http://www.whocc.no/atc_ddd_index/ http://www.whocc.no/atc_ddd_index/?code=$id A10BA02 metabolite 1 urn:miriam:atc ^\w(\d+)?(\w{1,2})?(\d+)?$ Anatomical Therapeutic Chemical 9 AntWeb http://www.antweb.org/ http://www.antweb.org/specimen.do?name=$id casent0106247 1 urn:miriam:antweb ^casent\d+$ AntWeb 10 ArachnoServer http://www.arachnoserver.org/ http://www.arachnoserver.org/toxincard.html?id=$id AS000060 1 urn:miriam:arachnoserver ^AS\d{6}$ ArachnoServer 6 11 ArrayExpress http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/arrayexpress/experiments/$id E-MEXP-1712 experiment 1 urn:miriam:arrayexpress ^[AEP]-\w{4}-\d+$ ArrayExpress 7 12 arXiv http://arxiv.org/ http://arxiv.org/abs/$id 0807.4956v1 publication 1 urn:miriam:arxiv ^(\w+(\-\w+)?(\.\w+)?/)?\d{4,7}(\.\d{4}(v\d+)?)?$ arXiv 13 BDGP insertion DB http://flypush.imgen.bcm.tmc.edu/pscreen/ http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$id KG09531 1 urn:miriam:BDGP.insertion ^\w+$ BDGP insertion DB 14 BeetleBase http://beetlebase.org/ http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$id TC010103 1 urn:miriam:beetlebase ^TC\d+$ BeetleBase 8 15 BIND http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id pathway 1 urn:miriam:bind ^\d+$ BIND 16 BioCatalogue http://www.biocatalogue.org/ http://www.biocatalogue.org/services/$id 614 1 urn:miriam:biocatalogue.service ^\d+$ BioCatalogue 17 BioCyc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX 1 urn:miriam:biocyc ^\w+$ BioCyc 9 18 BioCyc Bc http://www.biocyc.org http://www.biocyc.org/getid?id=$id EcoCyc:MON0-2657 gene 1 Bc (Meta|Eco)Cyc:.+ 10 19 BioGrid Bg http://www.thebiogrid.org/index.php http://www.thebiogrid.org/SearchResults/summary/$id 31623 probe 1 urn:miriam:biogrid ^\d+$ BioGRID 11 20 BioModels Database http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^(BIOMD|MODEL)\d{10}$ BioModels Database 12 21 BioNumbers http://www.bionumbers.hms.harvard.edu/search.aspx http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$id&ver=1 104674 experiment 1 urn:miriam:bionumbers ^\d+$ BioNumbers 13 BioSystems http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems 22 BioPortal http://bioportal.bioontology.org/ http://bioportal.bioontology.org/ontologies/$id 1046 1 urn:miriam:bioportal ^\d+$ BioPortal 23 BioSystems http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 001 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems 24 BOLD Taxonomy http://www.boldsystems.org/ http://www.boldsystems.org/views/taxbrowser.php?taxid=$id 27267 1 urn:miriam:bold.taxonomy ^\d+$ BOLD Taxonomy 14 25 Brenda Tissue Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id BTO:0000146 ontology 1 urn:miriam:obo.bto ^BTO:\d{7}$ Brenda Tissue Ontology 26 Candida Genome Database http://www.candidagenome.org/ http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$id CAL0003079 1 urn:miriam:cgd ^CAL\d{7}$ Candida Genome Database 15 27 CAS Ca http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id metabolite 1 Ca \d+-\d+-\d+ 28 CATH domain http://www.cathdb.info/ http://www.cathdb.info/domain/$id 1cukA01 1 urn:miriam:cath.domain ^\w+$ CATH domain 29 CATH superfamily http://www.cathdb.info/ http://www.cathdb.info/cathnode/$id 1.10.10.200 1 urn:miriam:cath.superfamily ^\d+\.\d+\.\d+\.\d+ CATH superfamily 30 CAZy http://www.cazy.org/ http://www.cazy.org/$id.html GT10 1 urn:miriam:cazy ^GT\d+$ CAZy 16 31 CCDS Cc http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS43989 probe 0 Cc 17 Cell Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id CL:0000232 ontology 1 urn:miriam:obo.clo ^CL:\d{7}$ Cell Ontology 32 Cell Cycle Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id CCO:P0000023 1 urn:miriam:cco ^CCO\:\w+$ Cell Cycle Ontology 33 Cell Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id CL:0000232 ontology 1 urn:miriam:obo.clo ^CL:\d{7}$ Cell Type Ontology 18 34 ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:obo.chebi ^CHEBI:\d+$ ChEBI 19 ChEMBL compound https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$id 210313 metabolite 1 urn:miriam:chembl.compound ^\d+$ ChEMBL compound 20 ChEMBL target https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembldb/index.php/target/inspect/$id 11031 protein 1 urn:miriam:chembl.target ^\d+$ ChEMBL target 21 Chemical Component Dictionary http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?APPLICATION=1 http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=$id&APPLICATION=1 AB0 ontology 1 urn:miriam:pdb-ccd ^\w{3}$ Chemical Component Dictionary 22 ChemIDplus http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id 57272 metabolite 1 urn:miriam:chemidplus ^\d+$ ChemIDplus 23 Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^/d+$ ChemSpider 35 ChemBank http://chembank.broadinstitute.org/ http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$id 1000000 1 urn:miriam:chembank ^\d+$ ChemBank 36 ChEMBL compound https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound 37 ChEMBL target https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembldb/index.php/target/inspect/$id CHEMBL3467 protein 1 urn:miriam:chembl.target ^CHEMBL\d+$ ChEMBL target 38 Chemical Component Dictionary http://www.ebi.ac.uk/pdbe-srv/pdbechem/ http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id AB0 ontology 1 urn:miriam:pdb-ccd ^\w{3}$ Chemical Component Dictionary 39 ChemIDplus http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id 000057272 metabolite 1 urn:miriam:chemidplus ^\d+$ ChemIDplus 40 Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider 24 41 Cint C probe 0 C 25 ClinicalTrials.gov http://clinicaltrials.gov/ http://clinicaltrials.gov/ct2/show/$id NCT00222573 experiment 1 ^NCT\d{8}$ ClinicalTrials.gov 42 ClinicalTrials.gov http://clinicaltrials.gov/ http://clinicaltrials.gov/ct2/show/$id NCT00222573 experiment 1 43 ClinicalTrials.gov http://clinicaltrials.gov/ http://clinicaltrials.gov/ct2/show/$id NCT00222573 1 urn:miriam:clinicaltrials ^NCT\d{8}$ ClinicalTrials.gov 26 44 CluSTr http://www.ebi.ac.uk/clustr/ http://www.ebi.ac.uk/clustr-srv/CCluster?interpro=yes&cluster_varid=$id HUMAN:55140:308.6 protein 1 urn:miriam:clustr ^[0-9A-Za-z]+:\d+:\d{1,5}(\.\d)?$ CluSTr 27 45 CodeLink Ge GE86325 probe 0 Ge 46 Compulyeast http://compluyeast2dpage.dacya.ucm.es/ http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$id O08709 1 urn:miriam:compulyeast ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ Compulyeast 28 47 Conserved Domain Database http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$id cd00400 protein 1 urn:miriam:cdd ^cd\d{5}$ Conserved Domain Database 48 CryptoDB http://cryptodb.org/cryptodb/ http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id cgd7_230 1 urn:miriam:cryptodb ^\w+ CryptoDB 49 CSA http://www.ebi.ac.uk/thornton-srv/databases/CSA/ http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/CSA/CSA_Site_Wrapper.pl?pdb=$id 1a05 1 urn:miriam:csa uniprot|pdb|EC code CSA 29 50 CTD Chemical http://ctd.mdibl.org/ http://ctd.mdibl.org/detail.go?type=chem&acc=$id D001151 metabolite 1 urn:miriam:ctd.chemical ^D\d+$ CTD Chemical 30 51 CTD Disease http://ctd.mdibl.org/ http://ctd.mdibl.org/detail.go?type=disease&db=MESH&acc=$id D053716 ontology 1 urn:miriam:ctd.disease ^D\d+$ CTD Disease 31 52 CTD Gene http://ctd.mdibl.org/ http://ctd.mdibl.org/basicQuery.go?bqCat=gene&bq=$id 101 gene 1 urn:miriam:ctd.gene ^\d+$ CTD Gene 53 CutDB http://cutdb.burnham.org http://cutdb.burnham.org/relation/show/$id 25782 1 urn:miriam:pmap.cutdb ^\d+$ CutDB 32 54 Database of Interacting Proteins http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N protein 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins 33 55 Database of Quantitative Cellular Signaling: Model http://doqcs.ncbs.res.in/ http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$id 57 pathway 1 urn:miriam:doqcs.model ^\d+$ Database of Quantitative Cellular Signaling: Model 34 56 Database of Quantitative Cellular Signaling: Pathway http://doqcs.ncbs.res.in/ http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$id 131 pathway 1 urn:miriam:doqcs.pathway ^\d+$ Database of Quantitative Cellular Signaling: Pathway 57 dbEST http://www.ncbi.nlm.nih.gov/nucest http://www.ncbi.nlm.nih.gov/nucest/$id BP100000 1 urn:miriam:dbest ^BP\d+$ dbEST 58 dbProbe http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe http://www.ncbi.nlm.nih.gov/projects/genome/probe/reports/probereport.cgi?uid=$id 1000000 1 urn:miriam:dbprobe ^\d+$ dbProbe 35 59 dbSNP Sn gene 1 Sn 60 dbSNP http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$id 121909098 1 urn:miriam:dbsnp ^\d+$ dbSNP 61 DisProt http://www.disprot.org/ http://www.disprot.org/protein.php?id=$id DP00001 1 urn:miriam:disprot ^DP\d{5}$ DisProt 36 62 DOI http://www.doi.org/ http://dx.doi.org/$id 10.1038/nbt1156 publication 1 urn:miriam:doi ^(doi\:)?\d{2}\.\d{4}/.*$ DOI 37 63 DrugBank http://www.drugbank.ca/ http://www.drugbank.ca/drugs/$id DB00001 metabolite 1 urn:miriam:drugbank ^DB\d{5}$ DrugBank 38 64 EC Number E http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$id 1.1.1.1 gene 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA 65 EchoBASE http://www.ecoli-york.org/ http://www.ecoli-york.org/Gene.cfm?recordID=$id EB0170 1 urn:miriam:echobase ^EB\d+$ EchoBASE 66 EcoGene http://ecogene.org/ http://ecogene.org/geneInfo.php?eg_id=$id EG10173 1 urn:miriam:ecogene ^EG\d+$ EcoGene 39 67 Ecoli Ec gene Escherichia coli 1 Ec 68 EDAM Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id EDAM:0001163 1 urn:miriam:edam EDAM:\d{7} EDAM Ontology 69 eggNOG http://eggnog.embl.de/version_3.0/ http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$id veNOG12876 1 urn:miriam:eggnog ^\w+$ eggNOG 40 70 EMBL Em http://www.ebi.ac.uk/embl/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+EntryPage+-e+[EMBL:$id]+-view+EmblEntry X58356 gene 1 urn:miriam:insdc ^\w+(\_)?\d+(\.\d+)?$ Nucleotide Sequence Database 41 71 Ensembl En http://www.ensembl.org/ http://www.ensembl.org/id/$id ENSG00000139618 gene 1 urn:miriam:ensembl ^ENS[A-Z]*[FPTG]\d{11}$ Ensembl 42 72 Ensembl B. subtilis EnBs http://www.ensembl.org http://bacteria.ensembl.org/Bacillus/B_subtilis/Gene/Summary?g=$id EBBACG00000000013 gene Bos taurus 1 EnBs EBBACG\d{11} 73 Ensembl Bacteria http://bacteria.ensembl.org/ http://bacteria.ensembl.org/id/$id EBESCT00000015660 1 urn:miriam:ensembl.bacteria ^EB\w+$ Ensembl Bacteria 43 74 Ensembl C. elegans EnCe http://www.ensembl.org http://www.ensembl.org/Caenorhabditis_elegans/Gene/Summary?g=$id Y42H9B.1 gene Caenorhabditis elegans 1 EnCe 44 75 Ensembl Chicken EnGg http://www.ensembl.org http://www.ensembl.org/Gallus_gallus/Gene/Summary?g=$id ENSGALG00000021736 gene Gallus gallus 1 EnGg ENSGALG\d{11} … … 48 79 Ensembl E. coli EnEc http://www.ensembl.org http://bacteria.ensembl.org/Escherichia_Shigella/E_coli_K12/Gene/Summary?g=$id EBESCG00000000010 gene Escherichia coli 1 EnEc EBESCG\d{11} 49 80 Ensembl Fruitfly EnDm http://www.ensembl.org http://www.ensembl.org/Drosophila_melanogaster/Gene/Summary?g=$id FBgn0032956 gene Drosophila melanogaster 1 EnDm FBgn\d{7} 81 Ensembl Fungi http://fungi.ensembl.org/ http://fungi.ensembl.org/id/$id CADAFLAT00006211 1 urn:miriam:ensembl.fungi ^\w+$ Ensembl Fungi 50 82 Ensembl Horse EnQc http://www.ensembl.org http://www.ensembl.org/Equus_caballus/Gene/Summary?g=$id ENSECAG00000026160 gene Equus caballus 1 EnQc ENSECAG\d{11} 51 83 Ensembl Human EnHs http://www.ensembl.org http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=$id ENSG00000139618 gene Homo sapiens 1 EnHs ENSG\d{11} 52 84 Ensembl M. tuberculosis EnMx http://www.ensembl.org http://bacteria.ensembl.org/Mycobacterium/M_tuberculosis_H37Rv/Gene/Summary?g=$id EBMYCG00000003122 gene Mycobacterium tuberculosis 1 EnMx EBMYCG\d{11} 85 Ensembl Metazoa http://metazoa.ensembl.org/ http://metazoa.ensembl.org/id/$id FBtr0084214 1 urn:miriam:ensembl.metazoa ^\w+(\.)?\d+$ Ensembl Metazoa 53 86 Ensembl Mosquito EnAg http://www.ensembl.org http://www.ensembl.org/Anopheles_gambiae/Gene/Summary?_q=$id AGAP006864 gene Anopheles gambiae 1 EnAg AGAP\d{6} 54 87 Ensembl Mouse EnMm http://www.ensembl.org http://www.ensembl.org/Mus_musculus/Gene/Summary?g=$id ENSMUSG00000017167 gene Mus musculus 1 EnMm ENSMUSG\d{11} 55 88 Ensembl Pig EnSs http://www.ensembl.org http://www.ensembl.org/Sus_scrofa/Gene/Summary?g=$id ENSSSCG00000004244 gene Sus scrofa 1 EnSs 89 Ensembl Plants http://plants.ensembl.org/ http://plants.ensembl.org/id/$id AT1G73965 1 urn:miriam:ensembl.plant ^\w+$ Ensembl Plants 90 Ensembl Protists http://protists.ensembl.org http://protists.ensembl.org/id/$id PFC0120w 1 urn:miriam:ensembl.protist ^\w+$ Ensembl Protists 56 91 Ensembl Rat EnRn http://www.ensembl.org http://www.ensembl.org/Rattus_norvegicus/Gene/Summary?g=$id ENSRNOG00000016648 gene Rattus norvegicus 1 EnRn ENSRNOG\d{11} 57 92 Ensembl Xenopus EnXt http://www.ensembl.org http://www.ensembl.org/Xenopus_tropicalis/Gene/Summary?g=$id ENSXETG00000029448 gene Xenopus tropicalis 1 EnXt ENSXETG\d{11} … … 59 94 Ensembl Zebrafish EnDr http://www.ensembl.org http://www.ensembl.org/Danio_rerio/Gene/Summary?g=$id ENSDARG00000024771 gene Danio rerio 1 EnDr ENSDARG\d{11} 60 95 Entrez Gene L http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=$id 100010 gene 1 urn:miriam:entrez.gene ^\d+$ Entrez Gene 61 Enzyme Nomenclature http://www.ebi.ac.uk/intenz/ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 protein 1 urn:miriam:ec-code ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\. \d+$ Enzyme Nomenclature96 Enzyme Nomenclature http://www.ebi.ac.uk/intenz/ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 protein 1 urn:miriam:ec-code ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ Enzyme Nomenclature 62 97 Evidence Code http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id ECO:0000006 ontology 1 urn:miriam:obo.eco ECO:\d{7}$ Evidence Code Ontology 63 98 FlyBase F http://www.flybase.org/ http://www.flybase.org/reports/$id.html FBgn0011293 gene Drosophila melanogaster 1 urn:miriam:flybase ^FB\w{2}\d{7}$ FlyBase 64 99 FMA http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id FMA:67112 ontology 1 urn:miriam:obo.fma ^FMA:\d+$ FMA 100 GABI http://gabi.rzpd.de/ http://gabi.rzpd.de/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$id&Mode=ShowBioObject 2679240 1 urn:miriam:gabi ^\w+$ GABI 101 Genatlas http://genatlas.medecine.univ-paris5.fr/ http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$id HBB 1 urn:miriam:genatlas ^\w+$ Genatlas 65 102 GenBank G probe 0 G (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) 66 103 Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 Gw \d+ 67 104 GeneDB http://www.genedb.org/ http://www.genedb.org/gene/$id Cj1536c gene 1 urn:miriam:genedb ^[\w\d\.-]*$ GeneDB 68 GeneOntology T http://www.ebi.ac.uk/ego/ http://www.ebi.ac.uk/ego/GTerm?id=$id GO:0006915 probe 1 urn:miriam:obo.go ^GO:\d{7}$ Gene Ontology 105 GeneFarm http://urgi.versailles.inra.fr/Genefarm/ http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$id 4892 1 urn:miriam:genefarm ^\d+$ GeneFarm 106 GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 probe 1 urn:miriam:obo.go ^GO:\d{7}$ Gene Ontology 107 GeneTree http://www.ensembl.org/ http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$id ENSGT00550000074763 1 urn:miriam:genetree ^ENSGT\d+$ GeneTree 69 108 GEO http://www.ncbi.nlm.nih.gov/geo/ http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$id GDS1234 experiment 1 urn:miriam:geo ^GDS\d+$ GEO 109 GiardiaDB http://giardiadb.org/giardiadb/ http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id GL50803_102438 1 urn:miriam:giardiadb ^\w+$ GiardiaDB 70 110 GlycomeDB http://www.glycome-db.org/showMenu.action?major=database http://www.glycome-db.org/database/showStructure.action?glycomeId=$id 1 metabolite 1 urn:miriam:glycomedb ^\d+$ GlycomeDB 111 GOA http://www.ebi.ac.uk/GOA/ http://www.ebi.ac.uk/QuickGO/GProtein?ac=$id P12345 1 urn:miriam:goa ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ GOA 112 GPCRDB http://www.gpcr.org/7tm/ http://www.gpcr.org/7tm/proteins/$id RL3R1_HUMAN 1 urn:miriam:gpcrdb ^\w+$ GPCRDB 71 113 Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360-TAIR-G gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5}\-TAIR\-G 114 Gramene genes http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0080039 1 urn:miriam:gramene.gene ^GR\:\d+$ Gramene genes 72 115 Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ 73 116 Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 probe 0 Gl 74 117 Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm 75 118 Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 probe 0 Gp 119 Gramene protein http://www.gramene.org/ http://www.gramene.org/db/protein/protein_search?protein_id=$id 78073 1 urn:miriam:gramene.protein ^\d+$ Gramene protein 120 Gramene QTL http://www.gramene.org/ http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$id CQG5 1 urn:miriam:gramene.qtl ^\w+$ Gramene QTL 76 121 Gramene Rice EnOj http://www.gramene.org/ http://www.gramene.org/Oryza_sativa_japonica/Gene/Summary?db=core;g=$id osa-MIR171a gene 1 EnOj 122 Gramene Taxonomy http://www.gramene.org/ http://www.gramene.org/db/ontology/search?id=$id GR_tax:013681 1 urn:miriam:gramene.taxonomy ^GR\_tax\:\d+$ Gramene Taxonomy 123 GreenGenes http://greengenes.lbl.gov/ http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$id 100000 1 urn:miriam:greengenes ^\d+$ GreenGenes 124 GRIN Plant Taxonomy http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$id 19333 1 urn:miriam:grin.taxonomy ^\d+$ GRIN Plant Taxonomy 125 H-InvDb Locus http://h-invitational.jp/hinv/ahg-db/index.jsp http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$id HIX0004394 1 urn:miriam:hinv.locus ^HIX\d{7}(\.\d+)?^ H-InvDb Locus 126 H-InvDb Protein http://h-invitational.jp/hinv/ahg-db/index.jsp http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$id HIP000030660 1 urn:miriam:hinv.protein ^HIP\d{9}(\.\d+)?^ H-InvDb Protein 127 H-InvDb Transcript http://h-invitational.jp/hinv/ahg-db/index.jsp http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$id HIT000195363 1 urn:miriam:hinv.transcript ^HIT\d{9}(\.\d+)?^ H-InvDb Transcript 128 HCVDB http://euhcvdb.ibcp.fr/euHCVdb/ http://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$id M58335 1 urn:miriam:hcvdb ^M\d{5}$ HCVDB 77 129 HGNC H http://www.genenames.org http://www.genenames.org/data/hgnc_data.php?match=$id DAPK1 gene Homo sapiens 1 H [A-Z][A-Z,0-9]+ 78 130 HGNC Accession number Hac http://www.genenames.org http://www.genenames.org/data/hgnc_data.php?hgnc_id=$id HGNC:2674 gene Homo sapiens 1 urn:miriam:hgnc HGNC:\d{1,5} HGNC 79 131 HMDB Ch http://www.hmdb.ca/ http://www.hmdb.ca/metabolites/$id HMDB00001 metabolite 1 urn:miriam:hmdb ^HMDB\d{5}$ HMDB 80 HOVERGEN http://pbil.univ-lyon1.fr/databases/hovergen.php http://pbil.univ-lyon1.fr/cgi-bin/acnuc-ac2tree?query=$id&db=HOVERGEN P10000 gene 1 urn:miriam:hovergen ^P\d{5}$ HOVERGEN 132 HOGENOM http://pbil.univ-lyon1.fr/databases/hogenom/ http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$id HBG284870 1 urn:miriam:hogenom ^\w+$ HOGENOM 133 HOMD Sequence Metainformation http://www.homd.org/index.php http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$id SEQF1003 1 urn:miriam:homd.seq ^SEQ\d+$ HOMD Sequence Metainformation 134 HOMD Taxonomy http://www.homd.org/index.php http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$id&view=dynamic 811 1 urn:miriam:homd.taxon ^\d+$ HOMD Taxonomy 135 HOVERGEN http://pbil.univ-lyon1.fr/databases/hovergen.php http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$id&db=HOVERGEN HBG004341 gene 1 urn:miriam:hovergen ^HBG\d+$ HOVERGEN 81 136 HsGene Hs gene Homo sapiens 1 Hs 82 ICD http://www.who.int/classifications/icd/en/ http://apps.who.int/classifications/apps/icd/icd10online/index.htm?navi.htm+$id C34 ontology 1 urn:miriam:icd ^[A-Z]\d+(\.[-\d+])?$ ICD 137 HSSP http://swift.cmbi.kun.nl/swift/hssp/ ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$id.hssp 102l 1 urn:miriam:hssp ^\d+$ HSSP 138 Human Disease Ontology http://bioportal.bioontology.org/ http://bioportal.bioontology.org/ontologies/1009/?p=terms&conceptid=$id DOID:11337 1 urn:miriam:obo.do ^DOID\:\d+$ Human Disease Ontology 139 ICD http://www.who.int/classifications/icd/en/ http://apps.who.int/classifications/icd10/browse/2010/en#/$id C34 ontology 1 urn:miriam:icd ^[A-Z]\d+(\.[-\d+])?$ ICD 83 140 Illumina Il ILMN_5668 probe 0 Il ILMN_\d+ 84 141 IMEx http://disber.net/imexdrupal/ http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$id IM-12080-80 pathway 1 urn:miriam:imex ^IM-\d+(-?)(\d+?)$ IMEx 85 142 IntAct http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 pathway 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct 143 Integrated Microbial Genomes Gene http://img.jgi.doe.gov/ http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$id 638309541 1 urn:miriam:img.gene ^\d+$ Integrated Microbial Genomes Gene 144 Integrated Microbial Genomes Taxon http://img.jgi.doe.gov/ http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$id 648028003 1 urn:miriam:img.taxon ^\d+$ Integrated Microbial Genomes Taxon 86 145 InterPro I http://www.ebi.ac.uk/interpro/ http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro 87 146 IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 probe 1 urn:miriam:ipi ^IPI\d{8}$ IPI 88 iRefWeb http://wodaklab.org/iRefWeb/ http://wodaklab.org/iRefWeb/interaction/show/$id 239002 pathway 1 urn:miriam:irefweb ^\d+$ iRefWeb 147 IRD Segment Sequence http://www.fludb.org/ http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$id CY077097 1 urn:miriam:ird.segment ^\w+(\_)?\d+(\.\d+)?$ IRD Segment Sequence 148 iRefWeb http://wodaklab.org/iRefWeb/ http://wodaklab.org/iRefWeb/interaction/show/$id 617102 pathway 1 urn:miriam:irefweb ^\d+$ iRefWeb 89 149 IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ Os12g0561000 gene 1 Ir Os\d{2}g\d+ 90 150 ISBN http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN 151 ISFinder http://www-is.biotoul.fr/i http://www-is.biotoul.fr/index.html?is_special_name=$id ISA1083-2 1 urn:miriam:isfinder ^IS\w+(\-\d)?^ ISFinder 152 Japan Collection of Microorganisms http://www.jcm.riken.go.jp/ http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$id 17254 1 urn:miriam:jcm ^\d+$ Japan Collection of Microorganisms 91 153 JWS http://jjj.biochem.sun.ac.za/index.html http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?keytype=modelname&keyword=$id curien pathway 1 urn:miriam:jws ^\w+$ JWS Online 92 154 Kegg Compound Ck http://www.genome.jp/kegg/ligand.html http://www.genome.jp/dbget-bin/www_bget?cpd:$id C12345 metabolite 1 urn:miriam:kegg.compound ^C\d+$ KEGG Compound … … 97 159 KEGG Pathway http://www.genome.jp/kegg/pathway.html http://www.genome.ad.jp/dbget-bin/www_bget?pathway+$id hsa00620 pathway 1 urn:miriam:kegg.pathway ^\w{2,3}\d{5}$ KEGG Pathway 98 160 KEGG Reaction http://www.genome.jp/kegg/reaction/ http://www.genome.jp/dbget-bin/www_bget?rn:$id R00100 protein 1 urn:miriam:kegg.reaction ^R\d+$ KEGG Reaction 99 KiSAO http://bioportal.bioontology.org/ http://bioportal.bioontology.org/ visualize/40844/?id=$id KISAO:0000057 ontology 1 urn:miriam:biomodels.kisao ^KISAO:\d+$ KiSAO161 KiSAO http://bioportal.bioontology.org/ http://bioportal.bioontology.org/ontologies/1410?p=terms&conceptid=kisao:$id KISAO_0000057 ontology 1 urn:miriam:biomodels.kisao ^KISAO_\d+$ KiSAO 100 162 Ligand Expo http://ligand-depot.rutgers.edu/index.html http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid ABC protein 1 urn:miriam:ligandexpo ^(\w){3}$ Ligand Expo 101 Ligand-Gated Ion Channel database http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$id.php 5HT3Arano protein 1 urn:miriam:lgic ^ /w+$ Ligand-Gated Ion Channel database163 Ligand-Gated Ion Channel database http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$id.php 5HT3Arano protein 1 urn:miriam:lgic ^\w+$ Ligand-Gated Ion Channel database 102 164 LIPID MAPS http://www.lipidmaps.org http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=$id LMFA01030001 metabolite 1 urn:miriam:lipidmaps ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?$ LIPID MAPS 103 165 LipidBank http://lipidbank.jp/index.html http://lipidbank.jp/cgi-bin/detail.cgi?id=$id BBA0001 metabolite 1 urn:miriam:lipidbank ^\w+\d+$ LipidBank 104 MACiE http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/ getPage.pl?id=$id M0001 protein 1 urn:miriam:macie ^M\d{4}$ MACiE166 MACiE 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 105 167 MaizeGDB Mg http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=$id acc1 gene Zea mays 1 Mg 168 MaizeGDB Locus http://www.maizegdb.org/ http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$id 25011 1 urn:miriam:maizegdb.locus ^\d+$ MaizeGDB Locus 106 169 MatrixDB http://matrixdb.ibcp.fr/ http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association P00747_P07355 pathway 1 urn:miriam:matrixdb.association ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ MatrixDB 107 170 Melanoma Molecular Map Project Biomaps http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$id 37 pathway 1 urn:miriam:mmmp:biomaps ^\d+$ Melanoma Molecular Map Project Biomaps … … 109 172 MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/searches/accession_report.cgi?id=$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgd ^MGI:\d+$ Mouse Genome Database 110 173 Microbial Protein Interaction Database http://www.jcvi.org/mpidb/about.php http://www.jcvi.org/mpidb/experiment.php?interaction_id=$id 172 pathway 1 urn:miriam:mpid ^\d+$ Microbial Protein Interaction Database 174 MicrosporidiaDB http://microsporidiadb.org/micro/ http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id ECU03_0820i 1 urn:miriam:microsporidia ^\w+$ MicrosporidiaDB 111 175 MINT http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 pathway 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT 176 miRBase mature sequence http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence 112 177 miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence 113 MIRIAM Resources http://www.ebi.ac.uk/miriam/ http://www.ebi.ac.uk/miriam/main/$id MIR:00000008 ontology 1 urn:miriam:miriam ^MIR:\d{8}$ MIRIAM Resources 178 MIRIAM Registry collection http://www.ebi.ac.uk/miriam/ http://www.ebi.ac.uk/miriam/main/$id MIR:00000008 1 urn:miriam:miriam.collection ^MIR:000\d{5}$ MIRIAM Registry collection 179 MIRIAM Registry resource http://www.ebi.ac.uk/miriam/ http://www.ebi.ac.uk/miriam/main/resources/$id MIR:00100005 1 urn:miriam:miriam.resource ^MIR:001\d{5}$ MIRIAM Registry resource 180 MIRIAM Resources http://www.ebi.ac.uk/miriam/ http://www.ebi.ac.uk/miriam/main/$id MIR:00000008 ontology 1 urn:miriam:miriam 114 181 ModelDB http://senselab.med.yale.edu/ModelDB/ http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$id 45539 pathway 1 urn:miriam:modeldb ^\d+$ ModelDB 115 182 Molecular Interactions Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id MI:0308 ontology 1 urn:miriam:obo.mi ^MI:\d{4}$ Molecular Interactions Ontology 116 183 Molecular Modeling Database http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$id 50885 pathway 1 urn:miriam:mmdb ^\d{1,5}$ Molecular Modeling Database 184 MycoBank http://www.mycobank.org/ http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=$id 349124 1 urn:miriam:mycobank ^\d+$ MycoBank 185 MycoBrowser leprae http://mycobrowser.epfl.ch/leprosy.html http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$id ML0224 1 urn:miriam:myco.lepra ^ML\w+$ MycoBrowser leprae 186 MycoBrowser marinum http://mycobrowser.epfl.ch/marinolist.html http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$id MMAR_2462 1 urn:miriam:myco.marinum "MMAR\w+$ MycoBrowser marinum 187 MycoBrowser smegmatis http://mycobrowser.epfl.ch/smegmalist.html http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$id MSMEG_3769 1 urn:miriam:myco.smeg ^MSMEG\w+$ MycoBrowser smegmatis 188 MycoBrowser tuberculosis http://tuberculist.epfl.ch/ http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id Rv1908c 1 urn:miriam:myco.tuber ^\w+$ MycoBrowser tuberculosis 117 189 NASC Gene N ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G 118 190 NCI Pathway Interaction Database: Pathway http://pid.nci.nih.gov/ http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id pi3kcipathway pathway 1 urn:miriam:pid.pathway ^\w+$ NCI Pathway Interaction Database: Pathway 191 NCIt http://ncit.nci.nih.gov/ http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$id C80519 1 urn:miriam:ncit ^C\d+$ NCIt 119 192 NeuroLex http://www.neurolex.org/wiki/Main_Page http://www.neurolex.org/wiki/$id Birnlex_721 ontology 1 urn:miriam:neurolex ^(Birnlex_|Sao)\d+$ NeuroLex 120 193 NeuroMorpho http://neuromorpho.org/neuroMorpho/index.jsp http://neuromorpho.org/neuroMorpho/neuron_info.jsp?neuron_name=$id Rosa2 experiment 1 urn:miriam:neuromorpho ^\w+$ NeuroMorpho 121 194 NeuronDB http://senselab.med.yale.edu/NeuronDB/ http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$id 265 experiment 1 urn:miriam:neurondb ^\d+$ NeuronDB 195 NITE Biological Research Center Catalogue http://www.nbrc.nite.go.jp/e/index.html http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$id 00001234 1 urn:miriam:nbrc ^\d+$ NITE Biological Research Center Catalogue 122 196 NuGO wiki Nw http://wiki.nugo.org/index.php/$id HMDB00001 metabolite 0 Nw 197 OMIA http://omia.angis.org.au/ http://omia.angis.org.au/$id/ 1000 1 urn:miriam:omia ^\d+$ OMIA 123 198 OMIM Om http://www.ncbi.nlm.nih.gov/omim/ http://www.ncbi.nlm.nih.gov/omim/$id 603903 gene 1 urn:miriam:omim ^[*#+%^]?\d{6}$ OMIM 124 199 Ontology for Biomedical Investigations http://obi-ontology.org/page/Main_Page http://ashby.csail.mit.edu/cgi-bin/obiterm?ref=$id OBI_0000225 ontology 1 urn:miriam:obo.obi ^OBI_\d{7}$ Ontology for Biomedical Investigations 125 Ontology of Physics for Biology http://bioportal.bioontology.org/ http://bioportal.bioontology.org/visualize/42330/?conceptid=OPB:$id OPB_00573 ontology 1 urn:miriam:opb ^OPB\:OPB_\d+$ Ontology of Physics for Biology 200 Ontology of Physics for Biology http://bioportal.bioontology.org/ http://bioportal.bioontology.org/ontologies/1141?p=terms&conceptid=OPB:$id OPB_00573 ontology 1 urn:miriam:opb ^OPB\:OPB_\d+$ Ontology of Physics for Biology 201 Orphanet http://www.orpha.net/consor/ http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$id 85163 1 urn:miriam:orphanet ^\d+$ Orphanet 202 OrthoDB http://cegg.unige.ch/orthodb4 http://cegg.unige.ch/orthodb/results?searchtext=$id Q9P0K8 1 urn:miriam:orthodb ^\w+$ OrthoDB 126 203 Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob 127 204 Other O gene 1 O 205 PaleoDB http://paleodb.org/ http://paleodb.org/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$id 83088 1 urn:miriam:paleodb ^\d+$ PaleoDB 128 206 PANTHER http://www.pantherdb.org/ http://www.pantherdb.org/panther/family.do?clsAccession=$id PTHR12345 protein 1 urn:miriam:panther ^PTHR\d{5}$ PANTHER 129 Pathway Commons http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 717762pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons207 Pathway Commons http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 485991 pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons 130 208 PATO http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id PATO:0001998 ontology 1 urn:miriam:obo.pato ^PATO:\d{7}$ PATO 131 PDB Pd http://www.pdb.org/ http://www.rcsb.org/pdb/explore/explore.do?structureId=$id 2gc4 protein 1 urn:miriam:pdb ^ \w{4}$ Protein Data Bank209 PDB Pd http://www.pdb.org/ http://www.rcsb.org/pdb/explore/explore.do?structureId=$id 2gc4 protein 1 urn:miriam:pdb ^[0-9][A-Z0-9]{3}$ Protein Data Bank 132 210 PeptideAtlas http://www.peptideatlas.org/ https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$id PAp00000009 protein 1 urn:miriam:peptideatlas ^PAp[0-9]{8}$ PeptideAtlas 211 Peroxibase http://peroxibase.toulouse.inra.fr/ http://peroxibase.toulouse.inra.fr/listing.php?action=view&id=$id 5282 1 urn:miriam:peroxibase ^\d+$ Peroxibase 133 212 Pfam Pf http://pfam.sanger.ac.uk/ http://pfam.sanger.ac.uk/family?entry=$id PF01234 protein 1 urn:miriam:pfam ^PF\d{5}$ Pfam 134 213 PharmGKB Disease http://www.pharmgkb.org/ http://www.pharmgkb.org/do/serve?objId=$id&objCls=Disease PA447218 ontology 1 urn:miriam:pharmgkb.disease ^PA\d+$ PharmGKB Disease 135 214 PharmGKB Drug http://www.pharmgkb.org/ http://www.pharmgkb.org/do/serve?objId=$id&objCls=Drug PA448710 metabolite 1 urn:miriam:pharmgkb.drug ^PA\d+$ PharmGKB Drug 136 215 PharmGKB Pathways http://www.pharmgkb.org/ http://www.pharmgkb.org/do/serve?objId=$id&objCls=Pathway PA146123006 pathway 1 urn:miriam:pharmgkb.pathways ^PA\d+$ PharmGKB Pathways 137 PhosphoSite Protein http://www.phosphosite.org/homeAction.do http://www.phosphosite.org/proteinAction.do?id=$id 12300 protein 1 urn:miriam:phosphosite.protein ^ /d{5}$ PhosphoSite Protein216 PhosphoSite Protein http://www.phosphosite.org/homeAction.do http://www.phosphosite.org/proteinAction.do?id=$id 12300 protein 1 urn:miriam:phosphosite.protein ^\d{5}$ PhosphoSite Protein 138 217 PhosphoSite Residue http://www.phosphosite.org/homeAction.do http://www.phosphosite.org/siteAction.do?id=$id 2842 protein 1 urn:miriam:phosphosite.residue ^\d+$ PhosphoSite Residue 218 PhylomeDB http://phylomedb.org/ http://phylomedb.org/?seqid=$id Phy000CLXM_RAT 1 urn:miriam:phylomedb ^\w+$ PhylomeDB 139 219 PIRSF http://pir.georgetown.edu/pirsf/ http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id PIRSF000100 protein 1 urn:miriam:pirsf ^PIRSF\d{6}$ PIRSF 140 220 PlantGDB Pl http://www.plantgdb.org/ PUT-157a-Vitis_vinifera-37378 gene 1 Q PUT-[\w\d-]+ 221 PlasmoDB http://plasmodb.org/plasmo/ http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id PF11_0344 1 urn:miriam:plasmodb ^\w+$ PlasmoDB 222 PMP http://www.proteinmodelportal.org/ http://www.proteinmodelportal.org/?pid=modelDetail&pmpuid=$id 1000011778810 1 urn:miriam:pmp ^\d+$ PMP 141 223 PRIDE http://www.ebi.ac.uk/pride/ http://www.ebi.ac.uk/pride/experimentLink.do?experimentAccessionNumber=$id 1 protein 1 urn:miriam:pride ^\d+$ PRIDE 142 224 ProDom http://prodom.prabi.fr/prodom/current/html/home.php http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$id PD10000 protein 1 urn:miriam:prodom ^PD\d+$ ProDom 143 PROSITE http://www.expasy.org/prosite/ http://www.expasy.org/cgi-bin/nicesite.pl?$id PS00001 protein 1 urn:miriam:prosite ^PS\d{5}$ PROSITE 225 PROSITE http://www.expasy.org/prosite/ http://prosite.expasy.org/$id PS00001 protein 1 urn:miriam:prosite ^PS\d{5}$ PROSITE 226 ProtClustDB http://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$id O80725 1 urn:miriam:protclustdb ^\w+$ ProtClustDB 227 Protein Model Database http://mi.caspur.it/PMDB/ http://www.caspur.it/PMDB/user/search.php?idsearch=$id PM0012345 1 urn:miriam:pmdb ^PM\d{7} Protein Model Database 144 228 Protein Modification Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id MOD:00001 ontology 1 urn:miriam:obo.psi-mod ^MOD:\d{5} Protein Modification Ontology 145 PubChem Cp http://pubchem.ncbi.nlm.nih.gov/ http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?db=pccompound&term=$id 100101 metabolite 1 urn:miriam:pubchem.compound ^\d+$ PubChem-compound 229 Protein Ontology http://pir.georgetown.edu/pro/pro.shtml http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$id PR:000000563 1 urn:miriam:obo.pr ^PR\:\d+$ Protein Ontology 230 ProtoNet Cluster http://www.protonet.cs.huji.ac.il/ http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$id 4349895 1 urn:miriam:protonet.cluster ^\d+$ ProtoNet Cluster 231 ProtoNet ProteinCard http://www.protonet.cs.huji.ac.il/ http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$id 16941567 1 urn:miriam:protonet.proteincard ^\d+$. ProtoNet ProteinCard 232 Pseudomonas Genome Database http://www.pseudomonas.com/ http://www.pseudomonas.com/getAnnotation.do?locusID=$id PSEEN0001 1 urn:miriam:pseudomonas ^P\w+$ Pseudomonas Genome Database 146 233 PubChem-bioassay http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$id 1018 metabolite 1 urn:miriam:pubchem.bioassay ^\d+$ PubChem-bioassay 147 PubChem-substance Cps http://pubchem.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=$id 100101 metabolite 1 urn:miriam:pubchem.substance ^\d+$ PubChem-substance 148 PubChem-compound Cpc http://pubchem.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=$id 100101 metabolite 1 urn:miriam:pubchem.compound ^\d+$ PubChem-compound 234 PubChem Cp http://pubchem.ncbi.nlm.nih.gov/ 100101 metabolite 1 ^\d+$ PubChem-compound 235 PubChem-compound Cpc http://pubchem.ncbi.nlm.nih.gov/ http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$id 100101 metabolite 1 urn:miriam:pubchem.compound ^\d+$ PubChem-compound 236 PubChem-substance Cps http://pubchem.ncbi.nlm.nih.gov/ http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$id 100101 metabolite 1 urn:miriam:pubchem.substance ^\d+$ PubChem-substance 149 237 PubMed http://www.ncbi.nlm.nih.gov/PubMed/ http://www.ncbi.nlm.nih.gov/pubmed/$id 16333295 publication 1 urn:miriam:pubmed ^\d+$ PubMed 238 PubMed Central http://www.ncbi.nlm.nih.gov/pmc/ http://www.ncbi.nlm.nih.gov/pmc/articles/$id/?tool=pubmed PMC3084216 1 urn:miriam:pmc PMC\d+ PubMed Central 150 239 Reactome Re http://www.reactome.org/ http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$id REACT_1590 pathway 1 urn:miriam:reactome ^REACT_\d+(\.\d+)?$ Reactome 240 REBASE http://rebase.neb.com/rebase/ http://rebase.neb.com/rebase/enz/$id.html 101 1 urn:miriam:rebase ^\d+$ REBASE 151 241 RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq 152 Relation Ontology http://www.obofoundry.org/ro/ http://www.obofoundry.org/ro/#$id OBO_REL:is_a ontology 1 urn:miriam:obo.ro ^OBO_REL:\w+ \_\w+$ Relation Ontology242 Relation Ontology http://www.obofoundry.org/ro/ http://www.obofoundry.org/ro/#$id OBO_REL:is_a ontology 1 urn:miriam:obo.ro ^OBO_REL:\w+$ Relation Ontology 153 243 RESID http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID 154 244 Rfam Rf http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?$id RF00066 gene 1 Rf RF\d+ 155 RGD R http://rgd.mcw.edu/ genes/http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database245 RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database 156 246 Rhea http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 protein 1 urn:miriam:rhea ^\d{5}$ Rhea 157 247 Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id LOC_Os04g54800 gene Oryza sativa 1 Os … … 159 249 SABIO-RK Kinetic Record http://sabiork.h-its.org/ http://sabiork.h-its.org/kineticLawEntry.jsp?kinlawid=$id 5046 experiment 1 urn:miriam:sabiork.kineticrecord ^\d+$ SABIO-RK Kinetic Record 160 250 SABIO-RK Reaction http://sabiork.h-its.org/ http://sabiork.h-its.org/index2.jsp?reac=$id 75 protein 1 urn:miriam:sabiork.reaction ^\d+$ SABIO-RK Reaction 161 Saccharomyces genome database pathways http:// www.yeastgenome.org/biocyc/ http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$id PWY3O-214 pathway Saccharomyces cerevisiae 1 urn:miriam:sgd.pathways ^PWY\w{2}\-\d{3}$ Saccharomyces genome database pathways162 sequence ontology http://www.sequenceontology.org/ http://www.sequenceontology.org/miso/current_release/term/$id SO:0000704 ontology 1 urn:miriam:obo.so ^SO:\d{7}$ sequence ontology251 Saccharomyces genome database pathways http://pathway.yeastgenome.org/ http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$id PWY3O-214 pathway Saccharomyces cerevisiae 1 urn:miriam:sgd.pathways ^PWY\w{2}\-\d{3}$ Saccharomyces genome database pathways 252 sequence ontology http://www.sequenceontology.org/ http://www.sequenceontology.org/miso/current_release/term/$id SO:0000704 ontology 1 urn:miriam:obo.so ^SO:\d{7}$ Sequence Ontology 163 253 SGD D http://www.yeastgenome.org/ http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=$id S000028457 gene 1 urn:miriam:sgd ^S\d+$ SGD 164 Signaling Gateway http://www.signaling-gateway.org/ http://www.signaling-gateway.org/molecule/query?afcsid=$id A001094 protein 1 urn:miriam:signaling-gateway A0\d+Signaling Gateway254 Signaling Gateway http://www.signaling-gateway.org/molecule http://www.signaling-gateway.org/molecule/query?afcsid=$id A001094 protein 1 urn:miriam:signaling-gateway A\d{6}$ Signaling Gateway 165 255 Small Molecule Pathway Database http://www.smpdb.ca/pathways http://pathman.smpdb.ca/pathways/$id/pathway SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database 166 256 SMART 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 257 Sol Genomics Network http://solgenomics.net/ http://solgenomics.net/phenome/locus_display.pl?locus_id=$id 0001 1 urn:miriam:sgn ^\d+$ Sol Genomics Network 167 258 SPRINT http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&display_opts=Prints&category=None&queryform=false®expr=off PR00001 protein 1 urn:miriam:sprint ^PR\d{5}$ SPRINT 259 SubstrateDB http://substrate.burnham.org/ http://substrate.burnham.org/protein/annotation/$id/html 1915 1 urn:miriam:pmap.substratedb ^\w+$ SubstrateDB 168 260 SubtiWiki http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 pathway 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki 169 Systems Biology Ontology http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:obo.sbo ^SBO:\d{7}$ Systems Biology Ontology 261 SWISS-MODEL http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL 262 Systems Biology Ontology http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:obo.sbo 263 Systems Biology Ontology http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 1 urn:miriam:biomodels.sbo ^SBO:\d{7}$ Systems Biology Ontology 170 264 T3DB http://www.t3db.org/ http://www.t3db.org/toxins/$id T3D0001 metabolite 1 urn:miriam:t3db ^T3D\d+$ T3DB 171 265 TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus … … 173 267 TAIR Protein http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?accession=$id AASequence:1009107926 protein 1 urn:miriam:tair.protein ^AASequence:\d{10}$ TAIR Protein 174 268 Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/ http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$id 9606 organism 1 urn:miriam:taxonomy ^\d+$ Taxonomy 175 TEDDY http://teddyontology.sourceforge.net/ http://bioportal.bioontology.org/ visualize/40985/?id=teddy%3A$id TEDDY_0000050ontology 1 urn:miriam:biomodels.teddy ^TEDDY_\d{7}$ TEDDY269 TEDDY http://teddyontology.sourceforge.net/ http://bioportal.bioontology.org/ontologies/1407?p=terms&conceptid=$id TEDDY_0000066 ontology 1 urn:miriam:biomodels.teddy ^TEDDY_\d{7}$ TEDDY 176 270 TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti 271 ToxoDB http://toxodb.org/toxo/ http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id TGME49_053730 1 urn:miriam:toxoplasma ^\w+$ ToxoDB 177 272 Transport Classification Database http://www.tcdb.org/ http://www.tcdb.org/search/result.php?tc=$id 5.A.1.1.1 protein 1 urn:miriam:tcdb ^\d+\.[A-Z]\.\d+\.\d+\.\d+$ Transport Classification Database 273 TrichDB http://trichdb.org/trichdb/ http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id TVAG_386080 1 urn:miriam:trichdb ^\w+$ TrichDB 274 TriTrypDB http://tritrypdb.org/tritrypdb/ http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id Tb927.8.620 1 urn:miriam:tritrypdb ^\w+(\.)?\w+(\.)?\w+ TriTrypDB 178 275 TTD Drug http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug 179 276 TTD Target http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target … … 184 281 Unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 urn:miriam:unipathway ^UPA\d{5}$ Unipathway 185 282 Uniprot/TrEMBL S http://www.ebi.uniprot.org/ http://www.ebi.uniprot.org/entry/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProt 283 UniSTS http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$id 456789 1 urn:miriam:unists ^\d+$ UniSTS 186 284 Unit Ontology http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit http://www.ebi.ac.uk/ontology-lookup/?termId=$id UO:0000080 ontology 1 urn:miriam:obo.unit ^UO:\d{7}? Unit Ontology 285 VectorBase http://www.vectorbase.org/ http://www.vectorbase.org/Genome/BRCGene/?gene=$id ISCW007415 1 urn:miriam:vectorbase ^\D{4}\d{6}(\-\D{2})?$ VectorBase 187 286 Wheat gene catalog Wc http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/sql?sql=select+distinct+genewgcreference.number+as+WGC,+reference.name+as+Reference,+reference.title+as+Title,+journal.name+as+Journal,+reference.volume+as+Volume,+reference.pages+as+Page+from+reference+inner+join+genewgcreference+on+genewgcreference.referenceid=reference.id+inner+join+journal+on+reference.journalid=journal.id+where+genewgcreference.number=$id 341 gene Triticum aestivum 1 Wc 188 287 Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 5S-Rrna-D1_(Triticum) gene Triticum aestivum 1 Wn … … 193 292 WormBase W http://www.wormbase.org/ http://www.wormbase.org/db/gene/gene?name=$id;class=Gene WBGene00000001 gene Caenorhabditis elegans 1 urn:miriam:wormbase ^WBGene\d{8}$ WormBase 194 293 Wormpep http://www.wormbase.org/db/seq/protein http://www.wormbase.org/db/seq/protein?name=$id CE28239 protein 1 urn:miriam:wormpep ^CE\d{5}$ Wormpep 294 Xenbase http://www.xenbase.org/ http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$id 922462 1 urn:miriam:xenbase ^\d+$ Xenbase 195 295 ZFIN Z http://zfin.org http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=$id ZDB-GENE-041118-11 gene Danio rerio 1 urn:miriam:zfin ZDB\-GENE\-\d+\-\d+ ZFIN Gene -
trunk/org.bridgedb.bio/src/org/bridgedb/bio/BioDataSource.java
r549 r560 153 153 public static final DataSource MIRBASE = DataSource.register ( 154 154 "Mb", "miRBase").asDataSource(); 155 public static final DataSource MIRBASE_MATURE = DataSource.register ( 156 "Mbm", "miRBase mature").asDataSource(); 155 157 public static final DataSource MAIZE_GDB = DataSource.register ( 156 158 "Mg", "MaizeGDB").asDataSource();
