Changeset 475
- Timestamp:
- 01/25/11 22:09:45 (16 months ago)
- Files:
-
- 1 modified
Legend:
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- Added
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trunk/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.txt
r472 r475 11 11 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 12 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/$id 001 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems13 BioSystems http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems 14 14 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 15 15 CAS Ca http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id metabolite 1 Ca \d+-\d+-\d+ … … 17 17 Cell Ontology http://www.ebi.ac.uk/ontology-lookup/ http://www.ebi.ac.uk/ontology-lookup/?termId=$id CL:0000232 ontology 1 urn:miriam:obo.clo ^CL:\d{7}$ Cell Ontology 18 18 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 http ://www.ebi.ac.uk/chembldb http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$id 210313 metabolite 1 urn:miriam:chembl.compound ^\d+$ ChEMBL compound20 ChEMBL target http ://www.ebi.ac.uk/chembldb http://www.ebi.ac.uk/chembldb/index.php/target/inspect/$id 11031 protein 1 urn:miriam:chembl.target ^\d+$ ChEMBL target19 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 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=$id 000057272 metabolite 1 urn:miriam:chemidplus ^\d+$ ChemIDplus23 Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html metabolite 1 Cs22 ChemIDplus http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$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 24 24 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 25 26 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 26 27 CodeLink Ge GE86325 probe 0 Ge … … 30 31 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 31 32 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 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 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 32 35 dbSNP Sn gene 1 Sn 33 36 DOI http://www.doi.org/ http://dx.doi.org/$id 10.1038/nbt1156 publication 1 urn:miriam:doi ^(doi\:)?\d{2}\.\d{4}/.*$ DOI … … 36 39 Ecoli Ec gene Escherichia coli 1 Ec 37 40 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 38 Ensembl En http://www.ensembl.org/ http://www.ensembl.org/ Homo_sapiens/Search/Results?species=all;q=$id ENSG00000139618 gene 1 urn:miriam:ensembl ^ENS[A-Z]*[FPTG]\d{11}$ Ensembl41 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 39 42 Ensembl B. subtilis EnBs http://www.ensembl.org http://bacteria.ensembl.org/Bacillus/B_subtilis/Gene/Summary?g=$id EBBACG00000000013 gene Bos taurus 1 EnBs EBBACG\d{11} 40 43 Ensembl C. elegans EnCe http://www.ensembl.org http://www.ensembl.org/Caenorhabditis_elegans/Gene/Summary?g=$id Y42H9B.1 gene Caenorhabditis elegans 1 EnCe … … 53 56 Ensembl Rat EnRn http://www.ensembl.org http://www.ensembl.org/Rattus_norvegicus/Gene/Summary?g=$id ENSRNOG00000016648 gene Rattus norvegicus 1 EnRn ENSRNOG\d{11} 54 57 Ensembl Xenopus EnXt http://www.ensembl.org http://www.ensembl.org/Xenopus_tropicalis/Gene/Summary?g=$id ENSXETG00000029448 gene Xenopus tropicalis 1 EnXt ENSXETG\d{11} 55 Ensembl Yeast EnSc http://www.ensembl.org http://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?g=$id YGR147C gene Saccharomyces cerevisiae 1 EnSc 58 Ensembl Yeast EnSc http://www.ensembl.org http://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?g=$id YGR147C gene Saccharomyces cerevisiae 1 EnSc Y[A-Z][RL]\d{3}[WC](?:\-[A-Z])? 56 59 Ensembl Zebrafish EnDr http://www.ensembl.org http://www.ensembl.org/Danio_rerio/Gene/Summary?g=$id ENSDARG00000024771 gene Danio rerio 1 EnDr ENSDARG\d{11} 57 60 Entrez Gene L http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=$id 100010 gene 1 urn:miriam:entrez.gene ^\d+$ Entrez Gene 58 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 Nomenclature 59 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 62 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 60 63 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 61 64 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 … … 72 75 Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 probe 0 Gp 73 76 Gramene Rice EnOj http://www.gramene.org/ http://www.gramene.org/Oryza_sativa_japonica/Gene/Summary?db=core;g=$id osa-MIR171a gene 1 EnOj 74 HGNC H http://www.genenames.org http://www.genenames.org/data/hgnc_data.php?match=$id DAPK1 gene Homo sapiens 1 H ^[A-Za-z][A-Za-z0-9]*$ HGNC75 HGNC Accession number Hac http://www.genenames.org http://www.genenames.org/data/hgnc_data.php?hgnc_id=$id HGNC:2674 gene Homo sapiens 1 urn:miriam:hgnc HGNC:\d{1,5} HGNC Accession number77 HGNC H http://www.genenames.org http://www.genenames.org/data/hgnc_data.php?match=$id DAPK1 gene Homo sapiens 1 H [A-Z][A-Z,0-9]+ 78 HGNC Accession number Hac http://www.genenames.org http://www.genenames.org/data/hgnc_data.php?hgnc_id=$id HGNC:2674 gene Homo sapiens 1 urn:miriam:hgnc HGNC:\d{1,5} HGNC 76 79 HMDB Ch http://www.hmdb.ca/ http://www.hmdb.ca/metabolites/$id HMDB00001 metabolite 1 urn:miriam:hmdb ^HMDB\d{5}$ HMDB 77 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 … … 86 89 IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ Os12g0561000 gene 1 Ir Os\d{2}g\d+ 87 90 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 88 JWS http://jjj.biochem.sun.ac.za/index.html http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?keytype=modelname& amp;keyword=$id curien pathway 1 urn:miriam:jws ^\w+$ JWS Online91 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 89 92 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 90 93 KEGG Drug http://www.genome.jp/kegg/drug/ http://www.genome.jp/dbget-bin/www_bget?dr:$id D00123 metabolite 1 urn:miriam:kegg.drug ^D\d+$ KEGG Drug … … 109 112 miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence 110 113 MIRIAM Resources http://www.ebi.ac.uk/miriam/ http://www.ebi.ac.uk/miriam/main/$id MIR:00000008 ontology 1 urn:miriam:miriam ^MIR:\d{8}$ MIRIAM Resources 111 ModelDB http://senselab.med.yale.edu/ModelDB/ http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$id 45539 1 urn:miriam:modeldb ^\d+$ ModelDB114 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 112 115 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 113 116 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 114 117 NASC Gene N ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G 118 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 115 119 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 116 120 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 117 NeuronDB http://senselab.med.yale.edu/NeuronDB/ http://senselab.med.yale.edu/NeuronDB/ ndbEavSum.asp?id=$id 265 experiment 1 urn:miriam:neurondb ^\d+$ NeuronDB121 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 118 122 NuGO wiki Nw http://wiki.nugo.org/index.php/$id HMDB00001 metabolite 0 Nw 119 123 OMIM Om http://www.ncbi.nlm.nih.gov/omim/ http://www.ncbi.nlm.nih.gov/omim/$id 603903 gene 1 urn:miriam:omim ^[*#+%^]?\d{6}$ OMIM … … 123 127 Other O gene 1 O 124 128 PANTHER http://www.pantherdb.org/ http://www.pantherdb.org/panther/family.do?clsAccession=$id PTHR12345 protein 1 urn:miriam:panther ^PTHR\d{5}$ PANTHER 125 Pathway Commons http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 68808pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons129 Pathway Commons http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 717762 pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons 126 130 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 127 131 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 Bank … … 161 165 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 162 166 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 167 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 163 168 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 164 169 T3DB http://www.t3db.org/ http://www.t3db.org/toxins/$id T3D0001 metabolite 1 urn:miriam:t3db ^T3D\d+$ T3DB … … 172 177 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 173 178 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 174 TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id Rv0064 gene Mycobacterium tuberculosis 1 Tb 179 TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id Rv0064 gene Mycobacterium tuberculosis 1 Tb Rv\d{4}(A|B|c|\.\d)? 175 180 UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d 176 181 UniGene U http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=1548618&SEARCH=$id Hs.553708 gene 1 U [A-Z][a-z][a-z]?\.\d+ … … 178 183 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 179 184 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 185 Unit Ontology http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit http://www.ebi.ac.uk/ontology-lookup/?termId=$id UO:0000080 ontology 1 urn:miriam:obo.unit ^UO:\d{7}? Unit Ontology 180 186 Wheat gene catalog Wc http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/sql?sql=select+distinct+genewgcreference.number+as+WGC,+reference.name+as+Reference,+reference.title+as+Title,+journal.name+as+Journal,+reference.volume+as+Volume,+reference.pages+as+Page+from+reference+inner+join+genewgcreference+on+genewgcreference.referenceid=reference.id+inner+join+journal+on+reference.journalid=journal.id+where+genewgcreference.number=$id 341 gene Triticum aestivum 1 Wc 181 187 Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 5S-Rrna-D1_(Triticum) gene Triticum aestivum 1 Wn 182 188 Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr 183 WikiGenes Wg http://www.wikigenes.org/ http://www.wikigenes.org/e/gene/e/$id.html 7157 gene 0 Wg \d+189 WikiGenes Wg http://www.wikigenes.org/ http://www.wikigenes.org/e/gene/e/$id.html 7157 gene 0 Wg 184 190 WikiPathways Wp http://www.wikipathways.org/ http://www.wikipathways.org/index.php/Pathway:$id WP100 pathway 1 urn:miriam:wikipathways WP\d{1,5} WikiPathways 185 191 Wikipedia Wi http://www.wikipedia.org http://en.wikipedia.org/wiki/$id Acetate metabolite 1 Wi
