org.bridgedb.bio.datasources.txt Maven / Gradle / Ivy
Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset
Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent
BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 urn:miriam:bind ^\d+$ BIND
BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc
BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID
BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database
BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 001 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems
BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA
BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands
CAS Ca http://commonchemistry.org http://commonchemistry.org/ChemicalDetail.aspx?ref=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS
CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS
ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound
ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI
Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider
CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink
Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins
dbSNP Sn http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$id 121909098 gene 1 urn:miriam:dbsnp ^\d+$ dbSNP
DrugBank Dr http://www.drugbank.ca/ http://www.drugbank.ca/drugs/$id DB00001 metabolite 1 urn:miriam:drugbank ^DB\d{5}$ DrugBank
EcoCyc Eco http://ecocyc.org/ http://ecocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=$id 325-BISPHOSPHATE-NUCLEOTIDASE-RXN interaction Escherichia coli 1 Eco EcoCyc
EcoGene Ec http://ecogene.org/ http://ecogene.org/geneInfo.php?eg_id=$id EG10173 gene Escherichia coli 1 urn:miriam:ecogene ^EG\d+$ EcoGene
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
Ensembl En http://www.ensembl.org/ http://ensemblgenomes.org/id/$id ENSG00000139618 gene 1 urn:miriam:ensembl ^ENS[A-Z]*[FPTG]\d{11}$ Ensembl
Ensembl B. subtilis EnBs http://www.ensembl.org http://bacteria.ensembl.org/Bacillus/B_subtilis/Gene/Summary?g=$id EBBACG00000000013 gene Bacillus subtilis 1 EnBs EBBACG\d{11} Ensembl
Ensembl C. elegans EnCe http://www.ensembl.org http://www.ensembl.org/Caenorhabditis_elegans/Gene/Summary?g=$id Y42H9B.1 gene Caenorhabditis elegans 1 EnCe Ensembl
Ensembl Chicken EnGg http://www.ensembl.org http://www.ensembl.org/Gallus_gallus/Gene/Summary?g=$id ENSGALG00000021736 gene Gallus gallus 1 EnGg ENSGALG\d{11} Ensembl
Ensembl Chimp EnPt http://www.ensembl.org http://www.ensembl.org/Pan_troglodytes/Gene/Summary?g=$id ENSPTRG00000036034 gene Pan troglodytes 1 EnPt ENSPTRG\d{11} Ensembl
Ensembl Cow EnBt http://www.ensembl.org http://www.ensembl.org/Bos_taurus/Gene/Summary?g=$id ENSBTAG00000043548 gene Bos taurus 1 EnBt ENSBTAG\d{11} Ensembl
Ensembl Dog EnCf http://www.ensembl.org http://www.ensembl.org/Canis_familiaris/Gene/Summary?g=$id ENSCAFG00000025860 gene Canis familiaris 1 EnCf ENSCAFG\d{11} Ensembl
Ensembl E. coli EnEc http://www.ensembl.org http://bacteria.ensembl.org/Escherichia_Shigella/E_coli_K12/Gene/Summary?g=$id EBESCG00000000010 gene Escherichia coli 1 EnEc EBESCG\d{11} Ensembl
Ensembl Fruitfly EnDm http://www.ensembl.org http://www.ensembl.org/Drosophila_melanogaster/Gene/Summary?g=$id FBgn0032956 gene Drosophila melanogaster 1 EnDm FBgn\d{7} Ensembl
Ensembl Horse EnQc http://www.ensembl.org http://www.ensembl.org/Equus_caballus/Gene/Summary?g=$id ENSECAG00000026160 gene Equus caballus 1 EnQc ENSECAG\d{11} Ensembl
Ensembl Human EnHs http://www.ensembl.org http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=$id ENSG00000139618 gene Homo sapiens 1 EnHs ENSG\d{11} Ensembl
Ensembl M. tuberculosis EnMx http://www.ensembl.org http://bacteria.ensembl.org/Mycobacterium/M_tuberculosis_H37Rv/Gene/Summary?g=$id EBMYCG00000003122 gene Mycobacterium tuberculosis 1 EnMx EBMYCG\d{11} Ensembl
Ensembl Mosquito EnAg http://www.ensembl.org http://www.ensembl.org/Anopheles_gambiae/Gene/Summary?_q=$id AGAP006864 gene Anopheles gambiae 1 EnAg AGAP\d{6} Ensembl
Ensembl Mouse EnMm http://www.ensembl.org http://www.ensembl.org/Mus_musculus/Gene/Summary?g=$id ENSMUSG00000017167 gene Mus musculus 1 EnMm ENSMUSG\d{11} Ensembl
Ensembl Pig EnSs http://www.ensembl.org http://www.ensembl.org/Sus_scrofa/Gene/Summary?g=$id ENSSSCG00000004244 gene Sus scrofa 1 EnSs ENSSSCG\d{11} Ensembl
Ensembl Plants EP http://plants.ensembl.org/ http://plants.ensembl.org/id/$id AT1G73965 gene 1 urn:miriam:ensembl.plant ^\w+$ Ensembl Plants
Ensembl Rat EnRn http://www.ensembl.org http://www.ensembl.org/Rattus_norvegicus/Gene/Summary?g=$id ENSRNOG00000016648 gene Rattus norvegicus 1 EnRn ENSRNOG\d{11} Ensembl
Ensembl Xenopus EnXt http://www.ensembl.org http://www.ensembl.org/Xenopus_tropicalis/Gene/Summary?g=$id ENSXETG00000029448 gene Xenopus tropicalis 1 EnXt ENSXETG\d{11} Ensembl
Ensembl Yeast EnSc http://www.ensembl.org http://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?g=$id YGR147C gene Saccharomyces cerevisiae 1 EnSc Y[A-Z][RL]\d{3}[WC](?:\-[A-Z])? Ensembl
Ensembl Zebrafish EnDr http://www.ensembl.org http://www.ensembl.org/Danio_rerio/Gene/Summary?g=$id ENSDARG00000024771 gene Danio rerio 1 EnDr ENSDARG\d{11} Ensembl
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
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
EPA CompTox Ect https://comptox.epa.gov/dashboard https://comptox.epa.gov/dashboard/$id DTXSID7020637 metabolite 1 Ect ^DTXSID\d{7}\d?$ EPA CompTox Dashboard
FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 gene Drosophila melanogaster 1 urn:miriam:flybase ^FB\w{2}\d{7}$ FlyBase
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank
Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki
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
Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360-TAIR-G gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5}\-TAIR\-G Gramene Arabidopsis
Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes
Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature
Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize
Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway
Gramene Rice EnOj http://www.gramene.org/ http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=$id osa-MIR171a gene 1 EnOj Gramene Rice
HGNC H http://www.genenames.org http://www.genenames.org/data/hgnc_data.php?match=$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol
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
HMDB Ch http://www.hmdb.ca/ http://www.hmdb.ca/metabolites/$id HMDB00001 metabolite 1 urn:miriam:hmdb ^HMDB(\d{2})?\d{5}$ HMDB
HomoloGene Hg http://www.ncbi.nlm.nih.gov/homologene/ http://www.ncbi.nlm.nih.gov/homologene/$id 1000 gene 1 urn:miriam:homologene ^\d+$ HomoloGene
HPRD Hp http://www.hprd.org/ interaction Homo sapiens 1 urn:miriam:hprd HPRD
Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina
InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey
IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct
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
IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 urn:miriam:ipi ^IPI\d{8}$ IPI
IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene
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
KEGG Drug Kd 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
KEGG Genes Kg http://www.genome.jp/kegg/genes.html http://www.genome.jp/dbget-bin/www_bget?$id syn:ssr3451 gene 1 urn:miriam:kegg.genes ^\w+:[\w\d\.-]*$ KEGG Genes
KEGG Glycan Kl http://www.genome.jp/kegg/glycan/ http://www.genome.jp/dbget-bin/www_bget?gl:$id G00123 metabolite 1 urn:miriam:kegg.glycan ^G\d+$ KEGG Glycan
KEGG Pathway Kp http://www.genome.jp/kegg/pathway.html http://www.genome.jp/dbget-bin/www_bget?pathway+$id hsa00620 pathway 1 urn:miriam:kegg.pathway ^\w{2,4}\d{5}$ KEGG Pathway
KEGG Reaction Rk http://www.genome.jp/kegg/reaction/ http://www.genome.jp/dbget-bin/www_bget?rn:$id R00100 pathway 1 urn:miriam:kegg.reaction ^R\d+$ KEGG Reaction
KNApSAcK Cks http://kanaya.aist-nara.ac.jp/KNApSAcK/ http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$id C00000001 metabolite 1 urn:miriam:knapsack ^C\d{8} KNApSAcK
LIPID MAPS Lm http://www.lipidmaps.org http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$id LMPR0102010012 metabolite 1 urn:miriam:lipidmaps ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{2}([0-9a-zA-Z]{2,8})?$ LIPID MAPS
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
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
MaizeGDB Mg http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=$id acc1 gene Zea mays 1 Mg MaizeGDB
MatrixDB Md http://matrixdb.ibcp.fr/ http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$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
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
MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgd ^MGI:\d+$ Mouse Genome Database
MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT
miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence
miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene
NCBI Protein Np http://www.ncbi.nlm.nih.gov/protein http://www.ncbi.nlm.nih.gov/protein/$id CAA71118.1 protein 1 urn:miriam:ncbiprotein ^\w+\d+(\.\d+)?$ NCBI Protein
NCI Pathway Interaction Database Pid 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
OMIM Om http://omim.org/ http://omim.org/entry/$id 603903 gene 0 urn:miriam:omim ^[*#+%^]?\d{6}$ OMIM
Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase
Other O gene 1 O Other
Pathway Commons Pc http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 485991 pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons
PDB Pd http://www.pdb.org/ http://www.rcsb.org/pdb/explore/explore.do?structureId=$id 2gc4 protein 0 urn:miriam:pdb ^[0-9][A-Za-z0-9]{3}$ Protein Data Bank
Pfam Pf http://pfam.sanger.ac.uk/ http://pfam.sanger.ac.uk/family/$id/ PF01234 protein 1 urn:miriam:pfam ^PF\d{5}$ Pfam
PharmGKB Drug Pgd http://www.pharmgkb.org/ http://www.pharmgkb.org/drug/$id PA448710 metabolite 1 urn:miriam:pharmgkb.drug ^PA\d+$ PharmGKB Drug
PharmGKB Gene Pgg http://www.pharmgkb.org/ http://www.pharmgkb.org/gene/$id PA131 gene 1 urn:miriam:pharmgkb.gene ^PA\w+$ PharmGKB Gene
PharmGKB Pathways Pgp http://www.pharmgkb.org/ http://www.pharmgkb.org/pathway/$id PA146123006 pathway 1 urn:miriam:pharmgkb.pathways ^PA\d+$ PharmGKB Pathways
PhosphoSite Protein Pp 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
PINA Pi http://cbg.garvan.unsw.edu.au/pina/ http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$id&showExtend=null Q13485 interaction 1 urn:miriam:pina ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ PINA
PlantGDB Pl http://www.plantgdb.org/ PUT-157a-Vitis_vinifera-37378 gene 1 Pl PUT-[\w\d-]+ PlantGDB
PubChem-bioassay Cpb http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$id 1018 metabolite 0 urn:miriam:pubchem.bioassay ^\d+$ PubChem-bioassay
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
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
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
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
RESID Res 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
Rfam Rf http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?$id RF00066 gene 1 Rf RF\d+ RFAM
RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database
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
Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id LOC_Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene
SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD
Small Molecule Pathway Database Sm 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
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
SPIKE Sk http://www.cs.tau.ac.il/~spike/ http://www.cs.tau.ac.il/~spike/maps/$id.html spike00001 interaction 1 urn:miriam:spike.map ^spike\d{5}$ SPIKE Map
SPRINT Spr 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
STRING Str http://string.embl.de/ http://string.embl.de/interactions/$id P53350 protein 1 urn:miriam:string ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ STRING
SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/protein/annotation/$id/html 1915 protein 0 urn:miriam:pmap.substratedb ^\d+$ SubstrateDB
SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki
SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM
SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SML:\d+$ SwissLipids
Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:biomodels.sbo ^SBO:\d{7}$ Systems Biology Ontology
TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus
TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR
TTD Drug Td 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
TTD Target Tt 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
TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id Rv0064 gene Mycobacterium tuberculosis 1 urn:miriam:myco.tuber Rv\d{4}(A|B|c|\.\d)? TubercuList
UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser
UniGene U http://www.ncbi.nlm.nih.gov/unigene http://www.ncbi.nlm.nih.gov/unigene?term=$id Hs.553708 gene 1 U [A-Z][a-z][a-z]?\.\d+ UniGene
Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 urn:miriam:unipathway ^UPA\d{5}$ Unipathway
Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL
Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 5S-Rrna-D1_(Triticum) gene Triticum aestivum 1 Wn Wheat gene names
Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs
WikiGenes Wg http://www.wikigenes.org/ http://www.wikigenes.org/e/gene/e/$id.html 7157 gene 0 urn:miriam:wikigenes WikiGenes
WikiPathways Wp http://www.wikipathways.org/ http://www.wikipathways.org/index.php/Pathway:$id WP100 pathway 1 urn:miriam:wikipathways WP\d{1,5}(_r\d+)? WikiPathways
Wikidata Wd http://www.wikidata.org https://www.wikidata.org/wiki/$id Q407962 metabolite 1 urn:miriam:wikidata ^Q\d+$ Wikidata
Wikipedia Wi http://www.wikipedia.org https://en.wikipedia.org/wiki/$id Acetate metabolite 0 urn:miriam:wikipedia.en ^.*$ Wikipedia
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
XMetDB Xm http://www.xmetdb.org/ http://www.xmetdb.org/xmetdb/protocol/$id XMETDB171 interaction 1 ^XMETDB\d+$ Xenobiotics Metabolism Database
ZFIN Z http://zfin.org http://zfin.org/action/marker/view/$id ZDB-GENE-041118-11 gene Danio rerio 1 urn:miriam:zfin ZDB\-GENE\-\d+\-\d+ ZFIN Gene
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