org.bridgedb.bio.datasources.tsv Maven / Gradle / Ivy
Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe
Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe
AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event
AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway
AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction
AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite
BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction
BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene
BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction
BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway
BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway
BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein
BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite
CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite
CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene
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 P592 chembl.compound metabolite
ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite
Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite
CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe
Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex
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 dip interaction
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 P6861 dbsnp gene
DrugBank Dr http://www.drugbank.ca/ http://www.drugbank.ca/drugs/$id DB00001 metabolite 1 urn:miriam:drugbank ^D(B|BSALT|BCAT)(\d{1})?\d{5}$ DrugBank P715 drugbank metabolite
DOI Pbd https://doi.org/ https://doi.org/$id 10.1038/s41597-020-0477-8 publication 1 urn:miriam:doi ^\d{2}\.\d{4}.*$ Digital Object Identifier P356 doi publication
EcoCyc Eco http://ecocyc.org/ http://ecocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=$id 1.1.1.127-RXN interaction Escherichia coli 1 Eco ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+-RXN EcoCyc ecocyc interaction
EcoGene Ec http://ecogene.org/ http://ecogene.org/geneInfo.php?eg_id=$id EG10173 gene Escherichia coli 1 urn:miriam:ecogene ^EG\d+$ EcoGene ecogene gene
EMBL Em http://www.ebi.ac.uk/embl/ http://www.ebi.ac.uk/ena/data/view/$id X58356 gene 1 urn:miriam:ena.embl ^[A-Z]+[0-9]+$ European Nucleotide Archive ena.embl gene
Ensembl En http://www.ensembl.org/ https://www.ensembl.org/id/$id ENSG00000139618 gene 1 urn:miriam:ensembl ^ENS[A-Z]*[FPTG]\d{11}$ Ensembl P594 ensembl gene
Entrez Gene L http://www.ncbi.nlm.nih.gov/gene http://www.ncbi.nlm.nih.gov/gene/$id 100010 gene 1 urn:miriam:ncbigene ^\d+$ Entrez Gene P351 ncbigene gene
Enzyme Nomenclature E http://www.ebi.ac.uk/intenz/ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id 1.1.1.1 gene 1 urn:miriam:ec-code ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ Enzyme Nomenclature P591 eccode gene
EPA CompTox Ect https://comptox.epa.gov/dashboard https://comptox.epa.gov/dashboard/$id DTXSID7020637 metabolite 1 Ect ^DTXSID(\d{2})?\d{7}\d?$ EPA CompTox Dashboard P3117 comptox metabolite
European Registry of Materials Nmerm https://nanocommons.github.io/identifiers/ ERM00000064 material 0 ^ERM\d{8}$ European Registry of Materials erm material
FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 gene Drosophila melanogaster 1 urn:miriam:fb ^FB\w{2}\d{7}$ FlyBase P3852 flybase gene
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene
Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene
GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology
Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene
Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite
HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
HGNC Accession number Hac http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$id 2674 gene Homo sapiens 1 urn:miriam:hgnc ^(HGNC:)?\d{1,5}$ HGNC P354 hgnc gene
HMDB Ch http://www.hmdb.ca/ http://www.hmdb.ca/metabolites/$id HMDB0000001 metabolite 1 urn:miriam:hmdb ^HMDB(\d{2})?\d{5}$ HMDB P2057 hmdb metabolite
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 P593 homologene gene
HPRD Hp http://www.hprd.org/ interaction Homo sapiens 1 urn:miriam:hprd HPRD hprd interaction
Human Disease Ontology Do http://www.disease-ontology.org https://disease-ontology.org/?id=$id DOID:11337 unknown Homo sapiens 1 urn:miriam:doid ^DOID\:\d+$ Disease Ontology doid unknown,ontology,disease
ICD-9 ICD9 http://www.who.int/classifications/icd/en/ http://www.icd9data.com/getICD9Code.ashx?icd9=$id 104 unknown Homo sapiens 1 ICD9 ^\d+$ International Classification of Diseases icd9 unknown
ICD-10 ICD10 http://www.who.int/classifications/icd/en/ http://apps.who.int/classifications/icd10/browse/2010/en#/{$id} C34 unknown Homo sapiens 1 ICD10 ^[A-Z]\d+(\.[-\d+])?$ International Classification of Diseases icd10 unknown
ICD-11 ICD11 http://www.who.int/classifications/icd/en/ 1A95 unknown Homo sapiens 1 ICD11 ^([A-Z]|\d)+(\d|[A-Z])\d+$ International Classification of Diseases icd11 unknown
Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina illumina.probe probe
InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite
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 intact interaction
InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein
IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene
ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$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 P212 isbn publication
ISSN issn https://portal.issn.org https://portal.issn.org/resource/ISSN/$id 1776-3045 publication 1 urn:miriam:issn ^\d{4}-\d{3}[\dX]$ ISSN P236 issn publication
Joint Research Center Nmjrc https://joint-research-centre.ec.europa.eu/scientific-tools-and-databases/jrc-nanomaterials-repository_en JRCNM01000a material 1 ^JRCNM.*$ material
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 P665 kegg.compound metabolite
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 P665 kegg.drug metabolite
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 P665 kegg.genes gene
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 P665 kegg.glycan metabolite
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 P665 kegg.pathway 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 P665 kegg.reaction pathway
KNApSAcK Cks http://kanaya.aist-nara.ac.jp/KNApSAcK/ http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$id C00000001 metabolite 1 urn:miriam:knapsack ^C\d{8} KNApSAcK P2064 knapsack metabolite
LIPID MAPS Lm http://www.lipidmaps.org https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessClassSearch&LMID=$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 P2063 lipidmaps metabolite
LipidBank Lb http://lipidbank.jp/index.html http://lipidbank.jp/cgi-bin/detail.cgi?id=$id BBA0001 metabolite 1 urn:miriam:lipidbank ^\w+\d+$ LipidBank lipidbank metabolite
MACiE Ma http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id M0001 protein 1 urn:miriam:macie ^M\d{4}$ MACiE macie protein
MaizeGDB Mg https://maizegdb.org/ https://maizegdb.org/gene_center/gene/$id acc1 gene Zea mays 1 Mg MaizeGDB maizegdb.locus gene
MatrixDB Md http://matrixdb.ibcp.fr/ http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association P00747_P07355 interaction 1 urn:miriam:matrixdb.association ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ MatrixDB matrixdb.association interaction
MeSH Me http://id.nlm.nih.gov/mesh/ http://id.nlm.nih.gov/mesh/$id C000100 other 1 urn:miriam:mesh ^(C|D)\d{6}$ Medical Subject Headings mesh disease,metabolite,gene,other
MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.uk/metabolights/$id MTBLC17170 metabolite 1 Ml ^MTBLC\d{1,6}$ MetaboLights Compounds P3890 metabolights metabolite
MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene
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 mint interaction
miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease
NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene 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 ncbiprotein 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 pid.pathway pathway
OMIM Om http://omim.org/ http://omim.org/entry/$id 603903 gene 0 urn:miriam:mim ^[*#+%^]?\d{6}$ OMIM P492 omim gene,disease
OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ ensembl gene
ORCID orcid https://orcid.org https://orcid.org/$id 0000-0002-5355-2576 other Homo sapiens 1 urn:miriam:orcid ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ ORCID P496 orcid other,author
Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orphanet other
Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene
Other O gene 1 O Other other
Pathway Commons Pc http://www.pathwaycommons.org/pc/ http://www.pathwaycommons.org/pc/record2.do?id=$id 485991 pathway 1 urn:miriam:pathwaycommons ^\d+$ Pathway Commons pathwaycommons pathway
Pathway Ontology PW http://bioportal.bioontology.org/ontologies/PW http://purl.bioontology.org/ontology/PW/PW:$id 0000208 pathway 1 urn:miriam:pw ^\d{7}$ Pathway Ontology P7333 pw pathway,ontology
PATO PATO http://bioportal.bioontology.org/ontologies/PATO http://purl.bioontology.org/ontology/PATO/PATO:$id 0001998 gene 1 urn:miriam:pato ^\d{7}$ PATO pato gene
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 P638 pdb protein
Pfam Pf https://pfam.xfam.org/ https://pfam.xfam.org/family/$id/ PF01234 protein 1 urn:miriam:pfam ^PF\d{5}$ Pfam P3519 pfam protein
PharmGKB Drug Pgd https://www.pharmgkb.org/ https://www.pharmgkb.org/drug/$id PA448710 metabolite 1 urn:miriam:pharmgkb.drug ^PA\d+$ PharmGKB Drug P7001 pharmgkb.drug metabolite
PharmGKB Gene Pgg https://www.pharmgkb.org/ https://www.pharmgkb.org/gene/$id PA131 gene 1 urn:miriam:pharmgkb.gene ^PA\w+$ PharmGKB Gene P7001 pharmgkb.gene gene
PharmGKB Pathways Pgp https://www.pharmgkb.org/ https://www.pharmgkb.org/pathway/$id PA146123006 pathway 1 urn:miriam:pharmgkb.pathways ^PA\d+$ PharmGKB Pathways P7001 pharmgkb.pathways pathway
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 phosphosite.protein 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 pina interaction
PlantGDB Pl http://www.plantgdb.org/ PUT-157a-Vitis_vinifera-37378 gene 1 Pl PUT-[\w\d-]+ PlantGDB gene
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.bioassay metabolite
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 P662 pubchem.compound metabolite
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 P2153 pubchem.substance metabolite
PubMed Pbm https://pubmed.ncbi.nlm.nih.gov/ https://pubmed.ncbi.nlm.nih.gov/$id 32169673 publication 1 urn:miriam:pubmed ^\d+$ PubMed Identifier P698 pubmed publication
PubMed Central Pmc https://www.ncbi.nlm.nih.gov/pmc/ https://www.ncbi.nlm.nih.gov/pmc/articles/$id PMC5461230 publication 1 urn:miriam:pmc ^PMC\d+$ PubMed Central Identifier P932 pmc publication
Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-HSA-201451 pathway 1 urn:miriam:reactome (^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$) Reactome P3937 reactome pathway
RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene
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 resid protein
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene
Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene
Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway
SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein
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 spike.map interaction
SPRINT Spr http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&display_opts=Prints&category=None&queryform=false®expr=off PR00001 protein 1 ^PR\d{5}$ SPRINT prints protein
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 string protein
SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/protein/annotation/$id/html 1915 protein 0 urn:miriam:pmap.substratedb ^\d+$ SubstrateDB pmap.substratedb protein
SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki subtiwiki gene
SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM supfam protein
SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein
SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite
Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology
TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene
TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene
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.drug metabolite
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 ttd.target protein
TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id Rv0064 gene Mycobacterium tuberculosis 1 urn:miriam:myco.tuber Rv\d{4}(A|B|c|\.\d)? TubercuList myco.tuber gene
UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser P2576 ucsc gene
UMLS CUI Cu https://www.nlm.nih.gov/research/umls/rxnorm/index.html https://www.ncbi.nlm.nih.gov/medgen/{$id} 760050 other Homo sapiens 1 urn:miriam:medgen ^[CN]*\d{4,7}$ MedGen medgen other
Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 ^UPA\d{5}$ Unipathway upa pathway
UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein
VMH metabolite VmhM http://www.vmh.life https://www.vmh.life/#metabolite/$id h2o metabolite 1 [a-zA-Z0-9_\(\_\)\[\]]+ VMH Life_Metabolite vmhmetabolite metabolite
Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 1-FEH+w3 gene Triticum aestivum 1 Wn Wheat gene names graingenes.symbol gene
Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs graingenes.reference gene
WikiGenes Wg http://www.wikigenes.org/ https://www.wikigenes.org/e/gene/e/$id.html 7157 gene 0 urn:miriam:wikigenes WikiGenes P351 wikigenes gene
WikiPathways Wp http://www.wikipathways.org/ https://www.wikipathways.org/instance/$id WP100 pathway 1 urn:miriam:wikipathways WP\d{1,5}(_r\d+)? WikiPathways P2410 wikipathways pathway,author
Wikidata Wd http://www.wikidata.org https://scholia.toolforge.org/$id Q407962 metabolite 1 urn:miriam:wikidata ^Q\d+$ Wikidata wikidata metabolite
Wikipedia Wi http://www.wikipedia.org https://en.wikipedia.org/wiki/$id Acetate metabolite 0 urn:miriam:wikipedia.en ^.*$ Wikipedia wikipedia.en metabolite
WormBase W http://www.wormbase.org/ http://www.wormbase.org/db/gene/gene?name=$id;class=Gene WBGene00000001 gene Caenorhabditis elegans 1 urn:miriam:wb ^WBGene\d{8}$ WormBase P3860 wormbase gene
XMetDB Xm http://www.xmetdb.org/ http://www.xmetdb.org/xmetdb/protocol/$id XMETDB171 interaction 1 ^XMETDB\d+$ Xenobiotics Metabolism Database xmetdb interaction
ZFIN Z http://zfin.org http://zfin.org/action/marker/view/$id ZDB-GENE-041118-11 gene Danio rerio 1 urn:miriam:zfin ZDB\-GENE\-\d+\-\d+ ZFIN Gene P3870 zfin gene
GitHub github https://github.com https://github.com/$id hbasaric author 0 urn:miriam:github ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ GitHub github author
Cell Ontology cl https://obophenotype.github.io/cell-ontology/ https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=$id 0000062 ontology 1 urn:miriam:cl ^\d{7}$ Cell ontology cl ontology,cell
Evidence Ontology EcOnt https://github.com/evidenceontology/evidenceontology/ https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=$id 0007807 ontology 1 urn:miriam:eco ^\d{7}$ Evidence ontology eco ontology,evidence
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