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
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
Affy	X	http://www.affymetrix.com/	http://www.ensembl.org/Homo_sapiens/Search/Results?species=all;feature=OligoProbe;q=$id	1851_s_at	probe		0	X	.+_at	
Agilent	Ag			A_24_P98555	probe		0	Ag	A_\d+_.+	
Anatomical Therapeutic Chemical		http://www.whocc.no/atc_ddd_index/	http://www.whocc.no/atc_ddd_index/?code=$id	A10BA02	metabolite		1	urn:miriam:atc	^(\w+(\-\w+)?(\.\w+)?/)?\d{4,7}(\.\d{4}(v\d+)?)?$	Anatomical Therapeutic Chemical
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
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
BIND		http://www.bind.ca/	http://www.bind.ca/Action?identifier=bindid&idsearch=$id		pathway		1	urn:miriam:bind	^\d+$	BIND
BioCyc	Bc	http://www.biocyc.org	http://www.biocyc.org/getid?id=$id	EcoCyc:MON0-2657	gene		1	Bc	(Meta|Eco)Cyc:.+	
BioGrid	Bg	http://www.thebiogrid.org/index.php	http://www.thebiogrid.org/SearchResults/summary/$id	31623	probe		1	urn:miriam:biogrid	^\d+$	BioGRID
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
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
BioSystems		http://www.ncbi.nlm.nih.gov/biosystems/	http://www.ncbi.nlm.nih.gov/biosystems/$id	1	pathway		1	urn:miriam:biosystems	^\d+$	BioSystems
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
CAS	Ca		http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id		metabolite		1	Ca	\d+-\d+-\d+	
CCDS	Cc		http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id	CCDS43989	probe		0	Cc		
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
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
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
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
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
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
Chemspider	Cs	http://www.chemspider.com/	http://www.chemspider.com/Chemical-Structure.$id.html	56586	metabolite		1	urn:miriam:chemspider	^/d+$	ChemSpider
Cint	C				probe		0	C		
ClinicalTrials.gov		http://clinicaltrials.gov/	http://clinicaltrials.gov/ct2/show/$id	NCT00222573	experiment		1		^NCT\d{8}$	ClinicalTrials.gov
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
CodeLink	Ge			GE86325	probe		0	Ge		
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
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
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
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
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
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
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
dbSNP	Sn				gene		1	Sn		
DOI		http://www.doi.org/	http://dx.doi.org/$id	10.1038/nbt1156	publication		1	urn:miriam:doi	^(doi\:)?\d{2}\.\d{4}/.*$	DOI
DrugBank		http://www.drugbank.ca/	http://www.drugbank.ca/drugs/$id	DB00001	metabolite		1	urn:miriam:drugbank	^DB\d{5}$	DrugBank
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
Ecoli	Ec				gene	Escherichia coli	1	Ec		
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
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
Ensembl B. subtilis	EnBs	http://www.ensembl.org	http://bacteria.ensembl.org/Bacillus/B_subtilis/Gene/Summary?g=$id	EBBACG00000000013	gene	Bos taurus	1	EnBs	EBBACG\d{11}	
Ensembl C. elegans	EnCe	http://www.ensembl.org	http://www.ensembl.org/Caenorhabditis_elegans/Gene/Summary?g=$id	Y42H9B.1	gene	Caenorhabditis elegans	1	EnCe		
Ensembl Chicken	EnGg	http://www.ensembl.org	http://www.ensembl.org/Gallus_gallus/Gene/Summary?g=$id	ENSGALG00000021736	gene	Gallus gallus	1	EnGg	ENSGALG\d{11}	
Ensembl Chimp	EnPt	http://www.ensembl.org	http://www.ensembl.org/Pan_troglodytes/Gene/Summary?g=$id	ENSPTRG00000036034	gene	Pan troglodytes	1	EnPt	ENSPTRG\d{11}	
Ensembl Cow	EnBt	http://www.ensembl.org	http://www.ensembl.org/Bos_taurus/Gene/Summary?g=$id	ENSBTAG00000043548	gene	Bos taurus	1	EnBt	ENSBTAG\d{11}	
Ensembl Dog	EnCf	http://www.ensembl.org	http://www.ensembl.org/Canis_familiaris/Gene/Summary?g=$id	ENSCAFG00000025860	gene	Canis familiaris	1	EnCf	ENSCAFG\d{11}	
Ensembl E. coli	EnEc	http://www.ensembl.org	http://bacteria.ensembl.org/Escherichia_Shigella/E_coli_K12/Gene/Summary?g=$id	EBESCG00000000010	gene	Escherichia coli	1	EnEc	EBESCG\d{11}	
Ensembl Fruitfly	EnDm	http://www.ensembl.org	http://www.ensembl.org/Drosophila_melanogaster/Gene/Summary?g=$id	FBgn0032956	gene	Drosophila melanogaster	1	EnDm	FBgn\d{7}	
Ensembl Horse	EnQc	http://www.ensembl.org	http://www.ensembl.org/Equus_caballus/Gene/Summary?g=$id	ENSECAG00000026160	gene	Equus caballus	1	EnQc	ENSECAG\d{11}	
Ensembl Human	EnHs	http://www.ensembl.org	http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=$id	ENSG00000139618	gene	Homo sapiens	1	EnHs	ENSG\d{11}	
Ensembl M. tuberculosis	EnMx	http://www.ensembl.org	http://bacteria.ensembl.org/Mycobacterium/M_tuberculosis_H37Rv/Gene/Summary?g=$id	EBMYCG00000003122	gene	Mycobacterium tuberculosis	1	EnMx	EBMYCG\d{11}	
Ensembl Mosquito	EnAg	http://www.ensembl.org	http://www.ensembl.org/Anopheles_gambiae/Gene/Summary?_q=$id	AGAP006864	gene	Anopheles gambiae	1	EnAg	AGAP\d{6}	
Ensembl Mouse	EnMm	http://www.ensembl.org	http://www.ensembl.org/Mus_musculus/Gene/Summary?g=$id	ENSMUSG00000017167	gene	Mus musculus	1	EnMm	ENSMUSG\d{11}	
Ensembl Pig	EnSs	http://www.ensembl.org	http://www.ensembl.org/Sus_scrofa/Gene/Summary?g=$id	ENSSSCG00000004244	gene	Sus scrofa	1	EnSs		
Ensembl Rat	EnRn	http://www.ensembl.org	http://www.ensembl.org/Rattus_norvegicus/Gene/Summary?g=$id	ENSRNOG00000016648	gene	Rattus norvegicus	1	EnRn	ENSRNOG\d{11}	
Ensembl Xenopus	EnXt	http://www.ensembl.org	http://www.ensembl.org/Xenopus_tropicalis/Gene/Summary?g=$id	ENSXETG00000029448	gene	Xenopus tropicalis	1	EnXt	ENSXETG\d{11}	
Ensembl Yeast	EnSc	http://www.ensembl.org	http://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?g=$id	YGR147C	gene	Saccharomyces cerevisiae	1	EnSc	Y[A-Z][RL]\d{3}[WC](?:\-[A-Z])?	
Ensembl Zebrafish	EnDr	http://www.ensembl.org	http://www.ensembl.org/Danio_rerio/Gene/Summary?g=$id	ENSDARG00000024771	gene	Danio rerio	1	EnDr	ENSDARG\d{11}	
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
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
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
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
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
GenBank	G				probe		0	G	(\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5})	
Gene Wiki	Gw	http://en.wikipedia.org/wiki/Portal:Gene_Wiki	http://plugins.gnf.org/cgi-bin/wp.cgi?id=$id	1017	gene		0	Gw	\d+	
GeneDB		http://www.genedb.org/	http://www.genedb.org/gene/$id	Cj1536c	gene		1	urn:miriam:genedb	^[\w\d\.-]*$	GeneDB
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
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
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
Gramene Arabidopsis	EnAt	http://www.gramene.org/	http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id	ATMG01360-TAIR-G	gene	Arabidopsis thaliana	1	EnAt	AT[\dCM]G\d{5}\-TAIR\-G	
Gramene Genes DB	Gg	http://www.gramene.org/	http://www.gramene.org/db/genes/search_gene?acc=$id	GR:0060184	gene		1	Gg	GR:\d+	
Gramene Literature	Gl	http://www.gramene.org/	http://www.gramene.org/db/literature/pub_search?ref_id=$id	6200	probe		0	Gl		
Gramene Maize	EnZm	http://www.ensembl.org	http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id	GRMZM2G174107	gene		1	EnZm		
Gramene Pathway	Gp	http://www.gramene.org/pathway		AAH72400	probe		0	Gp		
Gramene Rice	EnOj	http://www.gramene.org/	http://www.gramene.org/Oryza_sativa_japonica/Gene/Summary?db=core;g=$id	osa-MIR171a	gene		1	EnOj		
HGNC	H	http://www.genenames.org	http://www.genenames.org/data/hgnc_data.php?match=$id	DAPK1	gene	Homo sapiens	1	H	[A-Z][A-Z,0-9]+	
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{5}$	HMDB
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
HsGene	Hs				gene	Homo sapiens	1	Hs		
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
Illumina	Il			ILMN_5668	probe		0	Il	ILMN_\d+	
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
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
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=$id&format=default	IPI00000001	probe		1	urn:miriam:ipi	^IPI\d{8}$	IPI
iRefWeb		http://wodaklab.org/iRefWeb/	http://wodaklab.org/iRefWeb/interaction/show/$id	239002	pathway		1	urn:miriam:irefweb	^\d+$	iRefWeb
IRGSP Gene	Ir	http://rgp.dna.affrc.go.jp/IRGSP/		Os12g0561000	gene		1	Ir	Os\d{2}g\d+	
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
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
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		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		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 Orthology		http://www.genome.jp/kegg/ko.html	http://www.genome.jp/dbget-bin/www_bget?ko+$id	K00001	protein		1	urn:miriam:kegg.orthology	^K\d+$	KEGG Orthology
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
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
KiSAO		http://bioportal.bioontology.org/	http://bioportal.bioontology.org/visualize/40844/?id=$id	KISAO:0000057	ontology		1	urn:miriam:biomodels.kisao	^KISAO:\d+$	KiSAO
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
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
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
LipidBank		http://lipidbank.jp/index.html	http://lipidbank.jp/cgi-bin/detail.cgi?id=$id	BBA0001	metabolite		1	urn:miriam:lipidbank	^\w+\d+$	LipidBank
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=$id	M0001	protein		1	urn:miriam:macie	^M\d{4}$	MACiE
MaizeGDB	Mg		http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=$id	acc1	gene	Zea mays	1	Mg		
MatrixDB		http://matrixdb.ibcp.fr/	http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$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
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
MEROPS		http://merops.sanger.ac.uk/index.htm	http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=$id	S01.001	protein		1	urn:miriam:merops	^S\d{2}\.\d{3}$	MEROPS
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
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
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
miRBase Sequence	Mb	http://microrna.sanger.ac.uk/	http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=$id	MI0000001	gene		1	urn:miriam:mirbase	MI\d{7}	miRBase Sequence
MIRIAM Resources		http://www.ebi.ac.uk/miriam/	http://www.ebi.ac.uk/miriam/main/$id	MIR:00000008	ontology		1	urn:miriam:miriam	^MIR:\d{8}$	MIRIAM Resources
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
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
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
NASC Gene	N			ATMG00960-TAIR-G	gene	Arabidopsis thaliana	1	N	AT[\dCM]G\d{5}\-TAIR\-G	
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
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
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
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
NuGO wiki	Nw		http://wiki.nugo.org/index.php/$id	HMDB00001	metabolite		0	Nw		
OMIM	Om	http://www.ncbi.nlm.nih.gov/omim/	http://www.ncbi.nlm.nih.gov/omim/$id	603903	gene		1	urn:miriam:omim	^[*#+%^]?\d{6}$	OMIM
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
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
Oryzabase	Ob	http://www.shigen.nig.ac.jp/rice/oryzabase	http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id	468	gene	Oryza sativa	1	Ob		
Other	O				gene		1	O		
PANTHER		http://www.pantherdb.org/	http://www.pantherdb.org/panther/family.do?clsAccession=$id	PTHR12345	protein		1	urn:miriam:panther	^PTHR\d{5}$	PANTHER
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
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
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
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
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
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
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
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
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
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
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
PlantGDB	Pl	http://www.plantgdb.org/		PUT-157a-Vitis_vinifera-37378	gene		1	Q	PUT-[\w\d-]+	
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
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
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
Protein Modification Ontology		http://www.ebi.ac.uk/ontology-lookup/	http://www.ebi.ac.uk/ontology-lookup/?termId=$id	MOD:00001	ontology		1	urn:miriam:obo.psi-mod	^MOD:\d{5}	Protein Modification Ontology
PubChem	Cp	http://pubchem.ncbi.nlm.nih.gov/	http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?db=pccompound&term=$id	100101	metabolite		1	urn:miriam:pubchem.compound	^\d+$	PubChem-compound
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
PubChem-substance		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
PubMed		http://www.ncbi.nlm.nih.gov/PubMed/	http://www.ncbi.nlm.nih.gov/pubmed/$id	16333295	publication		1	urn:miriam:pubmed	^\d+$	PubMed
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
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 Ontology
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
Rfam	Rf		http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?$id	RF00066	gene		1	Rf	RF\d+	
RGD	R	http://rgd.mcw.edu/genes/	http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id	2018	gene	Rattus norvegicus	1	urn:miriam:rgd	^\d{4,7}$	Rat Genome Database
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
Rice Ensembl Gene	Os	http://www.gramene.org/Oryza_sativa	http://www.gramene.org/Oryza_sativa/geneview?gene=$id	LOC_Os04g54800	gene	Oryza sativa	1	Os		
SABIO-RK EC Record		http://sabiork.h-its.org/	http://sabiork.h-its.org/index2.jsp?EC=$id	2.7.1.1	protein		1	urn:miriam:sabiork.ec	^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$	SABIO-RK EC Record
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
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
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 pathways
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
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
Signaling Gateway		http://www.signaling-gateway.org/	http://www.signaling-gateway.org/molecule/query?afcsid=$id	A001094	protein		1	urn:miriam:signaling-gateway	A0\d+	Signaling Gateway
Small Molecule Pathway Database		http://www.smpdb.ca/pathways	http://pathman.smpdb.ca/pathways/$id/pathway	SMP00001	pathway		1	urn:miriam:smpdb	^SMP\d{5}$	Small Molecule Pathway Database
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
SPRINT		http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/	http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&display_opts=Prints&category=None&queryform=false&regexpr=off	PR00001	protein		1	urn:miriam:sprint	^PR\d{5}$	SPRINT
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
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
T3DB		http://www.t3db.org/	http://www.t3db.org/toxins/$id	T3D0001	metabolite		1	urn:miriam:t3db	^T3D\d+$	T3DB
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
TAIR Gene		http://arabidopsis.org/index.jsp	http://arabidopsis.org/servlets/TairObject?accession=$id	Gene:2200934	gene		1	urn:miriam:tair.gene	^Gene:\d{7}$	TAIR Gene
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
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
TEDDY		http://teddyontology.sourceforge.net/	http://bioportal.bioontology.org/visualize/40985/?id=teddy%3A$id	TEDDY_0000050	ontology		1	urn:miriam:biomodels.teddy	^TEDDY_\d{7}$	TEDDY
TIGR	Ti	http://www.jcvi.org/		12012.t00308	gene		1	Ti		
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
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
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
TubercuList	Tb	http://tuberculist.epfl.ch	http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id	Rv0064	gene	Mycobacterium tuberculosis	1	Tb	Rv\d{4}(A|B|c|\.\d)?	
UCSC Genome Browser	Uc	http://genome.ucsc.edu/	http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id	uc001tyh.1	gene		1	Uc	uc\d{3}[a-z]{3}\.\d	
UniGene	U	http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene	http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=1548618&SEARCH=$id	Hs.553708	gene		1	U	[A-Z][a-z][a-z]?\.\d+	
UniParc		http://www.ebi.ac.uk/uniparc/	http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$id	UPI000000000A	protein		1	urn:miriam:uniparc	^UPI[A-F0-9]{10}$	UniParc
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
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
Unit Ontology		http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit	http://www.ebi.ac.uk/ontology-lookup/?termId=$id	UO:0000080	ontology		1	urn:miriam:obo.unit	^UO:\d{7}?	Unit Ontology
Wheat gene catalog	Wc	http://wheat.pw.usda.gov/	http://wheat.pw.usda.gov/sql?sql=select+distinct+genewgcreference.number+as+WGC,+reference.name+as+Reference,+reference.title+as+Title,+journal.name+as+Journal,+reference.volume+as+Volume,+reference.pages+as+Page+from+reference+inner+join+genewgcreference+on+genewgcreference.referenceid=reference.id+inner+join+journal+on+reference.journalid=journal.id+where+genewgcreference.number=$id	341	gene	Triticum aestivum	1	Wc		
Wheat gene names	Wn	http://wheat.pw.usda.gov/	http://wheat.pw.usda.gov/report?class=gene;name=$id	5S-Rrna-D1_(Triticum)	gene	Triticum aestivum	1	Wn		
Wheat gene refs	Wr	http://wheat.pw.usda.gov/	http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id	WGS-95-1333	probe	Triticum aestivum	0	Wr		
WikiGenes	Wg	http://www.wikigenes.org/	http://www.wikigenes.org/e/gene/e/$id.html	7157	gene		0	Wg		
WikiPathways	Wp	http://www.wikipathways.org/	http://www.wikipathways.org/index.php/Pathway:$id	WP100	pathway		1	urn:miriam:wikipathways	WP\d{1,5}	WikiPathways
Wikipedia	Wi	http://www.wikipedia.org	http://en.wikipedia.org/wiki/$id	Acetate	metabolite		1	Wi		
WormBase	W	http://www.wormbase.org/	http://www.wormbase.org/db/gene/gene?name=$id;class=Gene	WBGene00000001	gene	Caenorhabditis elegans	1	urn:miriam:wormbase	^WBGene\d{8}$	WormBase
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
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
