LSRN Schema Registry

This Version
http://www.lsrn.org/lsrn/registry-2009-11-21-610 [.html] [.rdf]
Previous Stable Version
http://www.lsrn.org/lsrn/registry-2006-03-04-4319 [.html] [.rdf]
Latest Version
http://www.lsrn.org/lsrn/registry [.html] [.rdf]
Contributors
Sergei Egorov <esl@ariadnegenomics.com>

Copyright © 2006 LSRN Editors

GO.xrf_abbs Copyright © 1999-2006 the Gene Ontology Consortium

This work is licensed under a Creative Commons License.

Introduction

This registry lists Life Science Resource Name (LSRN) Schemas supported by LSRN.org's LSRN Resolver service. LSRN Schema defines a prefix (e.g. GO:), the format of the prefix dependent resource identifier, and associated metadata.

This registry is based on Gene Ontology Consortium's GO.xrf_abbs file (Revision 2.104), NCBI db_xref format specification (September 13, 2005) and many other sources, such as NCBI's Dbtag_db. Many records originated from GO.xrf_abbs file are incomplete and need additional curation; not all of them are suitable for automatic processing by LSRN resolver.

Table of Contents

A AceView_WormGenes, AGI_LocusCode, AGRICOLA_bib, AGRICOLA_IND, AGRICOLA_NAL, ASAP, ATCC, ATCC_dna, ATCC_in-host, Axeldb
B BDGP_EST, BDGP_INS, BIOMD, BIOSIS, BRENDA
C CAS, CBS, CDD, CGD, CGD_LOCUS, CGD_REF, CGEN, CGSC, CHEBI, ChEBI, CL, COG_Cluster, COG_Function, COG_Pathway
D dbEST, dbSNP, dbSTS, DDB, DDB_gene_name, DDB_REF, DDBJ, dictyBase, DragonDB_Allele, DragonDB_DNA, DragonDB_Locus, DragonDB_Protein
E EC, EcoCyc, ECOGENE, ECOGENE_G, EMBL, ENSEMBL, ENZYME, ESTLIB
F FANTOM_DB, FB, FLYBASE
G GABI, GB, GDB, GenBank, GeneDB, GeneDB_Gmorsitans, GeneDB_Lmajor, GeneDB_Pfalciparum, GeneDB_Spombe, GeneDB_Tbrucei, GeneID, GermOnline, GI, GO, GO_REF, GOA, GR, GR_MUT, GR_protein, GR_REF
H H-InvDB, H-invDB_cDNA, H-invDB_locus, HAMAP, HGNC, HGNC_Symbol, HSSP
I IFO, IMGT_GENE-DB, IMGT_HLA, IMGT_LIGM, InChI, INSD, IntAct, InterPro, IPI, ISBN, ISFinder, ISSN, IUPHAR
J JCM
K KEGG, KEGG_COMPOUND, KEGG_cpd, KEGG_dr, KEGG_DRUG, KEGG_ec, KEGG_hsa, KEGG_mmu, KEGG_path, KEGG_PATHWAY, KEGG_rno
L LIGAND, LocusID
M MaizeGDB, MaizeGDB_Locus, MEDLINE, MEROPS, MEROPS_fam, MeSH, MetaCyc, MGD, MGI, MIM, MIPS_funcat, MO
N NASC_code, NCBI_GB, NCBI_GP, NCBI_NM, NCBI_NP, NextDB, niaEST
O OMIM
P PDB, Pfam, PfamB, PGN, PIR, PIRSF, PMID, PO, Pompep, PRINTS, ProDom, Prosite, protein_id, PSEUDO, PubChem_Compound, PubChem_Substance
R RATMAP, Reactome, REBASE, RESID, RGD, RGDID, RiceGenes, RNAmods, RZPD
S SGD, SGD_LOCUS, SGD_REF, SMART, SoyBase, STKECM, STKECM_CMC, STKECM_CMP, SubtiList, SUBTILISTG
T TAIR, taxon, TC, TGD_LOCUS, TGD_REF, TIGR_Ath1, TIGR_CMR, TIGR_EGAD, TIGR_GenProp, TIGR_Pfa1, TIGR_REF, TIGR_Tba1, TIGR_TGI, TIGR_TIGRFAMS, TrEMBL
U UM-BBD_enzymeID, UM-BBD_pathwayID, UniGene, UNILIB, UniParc, UniProt, UniProtKB_Swiss-Prot, UniProtKB_TrEMBL
V VBASE2
W WB, WB_REF, WorfDB, WormBase, WP
Z ZFIN

Schemas

AceView_WormGenes:

Database: AceView Worm Genome

URL: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/

NCBI db_xref AceView/WormGenes
Primary subject gene
ID example vha-6
URL prefix http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?exdb=AceView&db=worm&term=

AGI_LocusCode:

Database: Arabidopsis Genome Initiative (TAIR, TIGR, MIPS)

URL: http://www.arabidopsis.org

Primary subject gene
Subject protein
ID example At2g17950
URL prefix http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=
URL prefix http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=
URL prefix http://arabidopsis.org/servlets/TairObject?type=locus&name=

AGRICOLA_bib:

Database: AGRICultural OnLine Access

URL: http://agricola.nal.usda.gov/

ID example bib=0000-05160

Editorial Notes

AGRICOLA_IND:

Database: AGRICultural OnLine Access

URL: http://agricola.cos.com/

ID example IND84014403

AGRICOLA_NAL:

Database: AGRICultural OnLine Access

URL: http://agricola.nal.usda.gov/

ID example TP248.2 P76 v.14

Editorial Notes

ASAP:

Database: A Systematic Annotation Package for Community Analysis of Genomes

URL: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm

ID example 8

Editorial Notes

ATCC:

Database: American Type Culture Collection database

URL: http://www.atcc.org/

ID example CCL-240
ID subject HL-60
URL prefix http://www.atcc.org/common/catalog/numSearch/numResults.cfm?collection=ce&ATCCNum=

ATCC_dna:

Database: American Type Culture Collection database

URL: http://www.atcc.org/

NCBI db_xref ATCC(dna)
Primary subject DNA
ID example CCL-64D
ID subject Mink genomic DNA (Mv 1 Lu)
URL prefix http://www.atcc.org/common/catalog/numSearch/numResults.cfm?collection=ce&ATCCNum=

ATCC_in-host:

Database: American Type Culture Collection database

URL: http://www.atcc.org/

NCBI db_xref ATCC(in host)
ID example 123456

Editorial Notes

Axeldb:

Database: A Xenopus laevis database

URL: http://www.dkfz-heidelberg.de/molecular_embryology/axeldb.htm

Primary subject gene
ID example 32B3.1
URL prefix http://indigene.ibaic.u-psud.fr/cgi-bin/ace/generic/tree/default?class=Locus&name=

BDGP_EST:

Database: Berkeley Drosophila Genome Project EST database

URL: http://www.fruitfly.org/EST/index.shtml

ID example 123456

Editorial Notes

BDGP_INS:

Database: Berkeley Drosophila Genome Project database -- Insertion

URL: http://www.fruitfly.org/

ID example 123456

Editorial Notes

BIOMD:

Database: BioModels Database

URL: http://www.ebi.ac.uk/biomodels/

ID example BIOMD0000000045
URL prefix http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=

BIOSIS:

Database: BIOSIS previews

URL: http://www.biosis.org/

ID example 200200247281

BRENDA:

Database: BRENDA, The Comprehensive Enzyme Information System

URL: http://www.brenda.uni-koeln.de/

ID example 4.2.1.3
URL prefix http://www.brenda.uni-koeln.de/php/result_flat.php4?ecno=

CAS:

Database: CAS Registry

URL: http://www.cas.org/

Primary subject chemical substance
ID type registry number
ID format up to 9 digits, divided by hyphens into 3 parts; the right digit is a checksum
ID example 58-08-2
ID subject caffeine
ID regexp [0-9]+[-][0-9]+[-][0-9]
URL regexp http://webbook.nist.gov/cgi/cbook.cgi?ID=&
URL regexp http://www.chemindustry.com/apps/chemicals?m=s\&t=&
RNEF property CAS ID

CBS:

Database: Center for Biological Sequence Analysis

URL: http://www.cbs.dtu.dk/

ID example NetNGlyc

Editorial Notes

CDD:

Database: Conserved Domain Database

URL: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

ID example pfam01484

CGD:

Database: Candida Genome Database

URL: http://www.candidagenome.org/

ID example CAL0005516
URL prefix http://www.candidagenome.org/cgi-bin/locus.pl?sgdid=

CGD_LOCUS:

Database: Candida Genome Database

URL: http://www.candidagenome.org/

ID example orf19.2475
URL prefix http://www.candidagenome.org/cgi-bin/locus.pl?locus=

Editorial Notes

CGD_REF:

Database: Candida Genome Database

URL: http://www.candidagenome.org/

ID example 1490
URL prefix http://www.candidagenome.org/cgi-bin/reference/reference.pl?refNo=

CGEN:

Database: Compugen Gene Ontology Gene Association Data

ID example PrID131022

CGSC:

Database: CGSC: E.coli Genetic Stock Center

URL: http://cgsc.biology.yale.edu/

ID example rbsK

Editorial Notes

CHEBI:

Database: Chemical Entities of Biological Interest (ChEBI) database of small molecules

URL: http://www.ebi.ac.uk/chebi/

Primary subject chemical compound
ID type sequential identifier
ID format positive numeral
ID example 27732
ID subject caffeine
ID regexp [1-9][0-9]*
URL prefix http://www.ebi.ac.uk/chebi/searchId.do?chebiId=

ChEBI:

Redirect to: CHEBI:

CL:

Database: Cell Type Ontology

URL: http://lists.sourceforge.net/lists/listinfo/obo-cell-type

ID example 0000041

COG_Cluster:

Database: NCBI COG cluster

URL: http://www.ncbi.nlm.nih.gov/COG/

ID example COG0001
URL prefix http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=

COG_Function:

Database: NCBI COG function

URL: http://www.ncbi.nlm.nih.gov/COG/

ID example H
URL prefix http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?fun=

COG_Pathway:

Database: NCBI COG pathway

URL: http://www.ncbi.nlm.nih.gov/COG/

ID example 14
URL prefix http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=

dbEST:

Database: EST database maintained at the NCBI

URL: http://www.ncbi.nlm.nih.gov/dbEST/index.html

ID example BP535535

dbSNP:

Database: Variation database maintained at the NCBI

URL: http://www.ncbi.nlm.nih.gov/SNP/

ID example rs133073

dbSTS:

Database: STS database maintained at the NCBI

URL: http://www.ncbi.nlm.nih.gov/dbSTS/index.html

ID example BV210161

DDB:

Database: DictyBase

URL: http://dictybase.org

ID example DDB0001836
URL prefix http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=

DDB_gene_name:

Database: DictyBase

URL: http://dictybase.org

ID example mlcE
URL prefix http://dictybase.org/db/cgi-bin/gene_page.pl?gene_name=

DDB_REF:

Database: DictyBase literature references

URL: http://dictybase.org

ID example 10157
URL prefix http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=

DDBJ:

Redirect to: INSD:

dictyBase:

Database: Dictyostelium genome database

URL: http://dictybase.org/

ID example DDB0191090

DragonDB_Allele:

Database: Antirrhinum majus genome database Allele

URL: http://www.antirrhinum.net/

Primary subject gene
ID example cho
URL prefix http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?class=Allele;name=

DragonDB_DNA:

Database: Antirrhinum majus genome database DNA Sequence

URL: http://www.antirrhinum.net/

Primary subject DNA
ID example 3hB06
URL prefix http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?class=Sequence;name=

DragonDB_Locus:

Database: Antirrhinum majus genome database Locus

URL: http://www.antirrhinum.net/

Primary subject gene
ID example DEF
URL prefix http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?class=Locus;name=

DragonDB_Protein:

Database: Antirrhinum majus genome database Protein

URL: http://www.antirrhinum.net/

Primary subject protein
ID example AMDEFA
URL prefix http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?class=Protein;name=

EC:

Database: The IUBMB Enzyme Commission

URL: http://www.chem.qmw.ac.uk/iubmb/enzyme/

Primary subject enzyme
ID type registry number
ID format N.N.N.N where N is either a number or '-'
ID example 3.4.11.4
ID subject tripeptide aminopeptidase
ID regexp ([0-9]+|[-])[.]([0-9]+|[-])[.]([0-9]+|[-])[.]([0-9]+|[-])
URL prefix http://www.genome.ad.jp/dbget-bin/www_bget?ec:
RNEF property EC Number

Editorial Notes

EcoCyc:

Database: The Encylopedia of E. coli metabolism

URL: http://ecocyc.org/

ID example P2-PWY
URL prefix http://malibu.ai.sri.com:1555/ECOLI/new-image?type=PATHWAY&object=?

ECOGENE:

Database: CGSC: E.coli Genetic Stock Center

URL: http://cgsc.biology.yale.edu/

ID example EG10818

Editorial Notes

ECOGENE_G:

Database: CGSC: E.coli Genetic Stock Center

URL: http://cgsc.biology.yale.edu/

ID example deoC

EMBL:

Redirect to: INSD:

ENSEMBL:

Database: Database of automatically annotated genomic data

URL: http://www.ensembl.org

ID example HUMAN-Gene-ENSG00000007102
URL prefix http://www.ensembl.org/perl/protview?peptide=

ENZYME:

Database: The Swiss Institute of Bioinformatics database of Enzymes

URL: http://www.expasy.ch/

ID example 1.1.1.1
URL prefix http://www.expasy.ch/cgi-bin/nicezyme.pl?

Editorial Notes

ESTLIB:

Database: EBI's EST library identifier

ID example 1200

FANTOM_DB:

Database: Database of Functional Annotation of Mouse

URL: http://fantom.gsc.riken.go.jp/

ID example 0610005A07

FB:

Database: FlyBase

URL: http://flybase.bio.indiana.edu/

ID example FBgn0000024
URL prefix http://fly.ebi.ac.uk:7081/.bin/fbidq.html?
URL prefix http://flybase.bio.indiana.edu/.bin/fbidq.html?

Editorial Notes

FLYBASE:

Database: Database of Genetic and molecular data of Drosophila

URL: http://www.flybase.org/

ID example FBgn0000024
URL prefix http://flybase.bio.indiana.edu/.bin/fbidq.html?
URL prefix http://fly.ebi.ac.uk:7081/.bin/fbidq.html?

Editorial Notes

GABI:

Database: Network of Different Plant Genomic Research Projects

URL: https://gabi.rzpd.de/

ID example HA05J18

GB:

Redirect to: INSD:

GDB:

Database: Human Genome Database accession numbers

URL: http://www.gdb.org/

ID example G00-128-600
URL prefix http://www.gdb.org/gdb-bin/genera/accno?accessionNum=

Editorial Notes

GenBank:

Redirect to: INSD:

GeneDB:

Database: Curated gene database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei

URL: http://www.genedb.org/

ID example SPCC285.16c
URL prefix http://www.genedb.org/genedb/Search?organism=All%3A*&name=

GeneDB_Gmorsitans:

Database: GeneDB_Gmorsitans

URL: http://www.genedb.org/glossina

ID example Gmm-0142
URL prefix http://www.genedb.org/genedb/Search?organism=glossina&name=

GeneDB_Lmajor:

Database: GeneDB_Lmajor

URL: http://www.genedb.org/leish

ID example LM5.32
URL prefix http://www.genedb.org/genedb/Search?organism=leish&name=

GeneDB_Pfalciparum:

Database: GeneDB_Pfalciparum

URL: http://www.genedb.org/malaria

ID example PFD0755c
URL prefix http://www.genedb.org/genedb/Search?organism=malaria&name=

GeneDB_Spombe:

Database: GeneDB_Spombe

URL: http://www.genedb.org/pombe

ID example SPAC890.04C
URL prefix http://www.genedb.org/genedb/Search?organism=pombe&name=

GeneDB_Tbrucei:

Database: GeneDB_Tbrucei

URL: http://www.genedb.org/tryp

ID example Tb927.1.5250
URL prefix http://www.genedb.org/genedb/Search?organism=tryp&name=

GeneID:

Database: Entrez Gene Database (replaces NCBI Locus Link)

URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

Primary subject gene
ID type sequential identifier
ID format positive numeral
ID example 7157
ID subject tumor protein p53
ID regexp [1-9][0-9]*
URL prefix http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=
RNEF property LocusLink ID

GermOnline:

Database: GermOnline

URL: http://www.germonline.org/

ID example 140116
URL prefix http://germonline.unibas.ch/gene_page.php?orf_id=
URL prefix http://germonline.yeastgenome.org/gene_page.php?orf_id=
URL prefix http://germonline.biochem.s.u-tokyo.ac.jp/gene_page.php?orf_id=

GI:

Database: GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins

ID example 1234567890

Editorial Notes

GO:

Database: Gene Ontology Database

URL: http://www.geneontology.org/

Primary subject concept
ID type sequential identifier
ID format 7-digit numeral
ID example 0006915
ID subject apoptosis
ID regexp [0-9]{7}
URL prefix http://godatabase.org/cgi-bin/go.cgi?query=GO:
RNEF property GO ID

GO_REF:

Database: Gene Ontology Database references

ID example 0000001

GOA:

Database: Gene Ontology Annotation Database Identifier

URL: http://www.ebi.ac.uk/GOA/

ID example P01100

GR:

Database: Gramene: A Comparative Mapping Resource for Grains

URL: http://www.gramene.org/

ID example P93436
URL prefix http://www.gramene.org/perl/protein_search?acc=

GR_MUT:

Database: Gramene: A Comparative Mapping Resource for Grains

URL: http://www.gramene.org/

ID example 659
URL prefix http://www.gramene.org/db/mutant/search_mutant?id=

Editorial Notes

GR_protein:

Database: Gramene: A Comparative Mapping Resource for Grains.

URL: http://www.gramene.org/

ID example 110916
URL prefix http://www.gramene.org/db/protein/protein_search?protein_id=

GR_REF:

Database: Gramene: A Comparative Mapping Resource for Grains

URL: http://www.gramene.org/

ID example 659
URL prefix http://www.gramene.org/perl/pub_search?ref_id=

H-InvDB:

Database: H-Invitational Database

URL: http://www.h-invitational.jp

ID example HIX0000001

H-invDB_cDNA:

Database: H-invitational Database

URL: http://www.h-invitational.jp/

ID example AK093148
URL prefix http://www.h-invdb.jbic.or.jp/soup/pub_Detail.pl?acc_id=
URL prefix http://www.jbirc.aist.go.jp/hinv/soup/pub_Detail.pl?acc_id=

H-invDB_locus:

Database: H-invitational Database

URL: http://www.h-invitational.jp/

ID example HIX0014446
URL prefix http://www.h-invdb.jbic.or.jp/soup/pub_Locus.pl?locus_id=
URL prefix http://www.jbirc.aist.go.jp/hinv/soup/pub_Locus.pl?locus_id=

HAMAP:

Database: High-quality Automated and Manual Annotation of microbial Proteomes

URL: http://us.expasy.org/sprot/hamap/

ID example MF_00031
URL prefix http://us.expasy.org/unirules/

HGNC:

Database: HUGO Gene Nomenclature Committee

URL: http://www.gene.ucl.ac.uk/nomenclature/

Primary subject gene
ID type sequential identifier
ID format positive numeral
ID example 11998
ID subject tumor protein p53
ID regexp [1-9][0-9]*
URL prefix http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:
RNEF property HGNC ID

Editorial Notes

HGNC_Symbol:

Database: HUGO Gene Nomenclature Committee

URL: http://www.gene.ucl.ac.uk/nomenclature/

Primary subject gene
ID type symbol
ID format a unique series of Latin (upper case in human) letters and Arabic numbers which usually is no longer than six characters in length; case-sensitive
ID example BRCA1
ID subject breast cancer, early onset 1
URL prefix http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=all_text&anchor=equals&symbol_search=Search&number=50&format=html&sortby=symbol&match=
RNEF property HUGO Symbol

HSSP:

Database: Database of homology-derived secondary structure of proteins

URL: http://www.sander.ebi.ac.uk/hssp/

ID example 12GS

IFO:

Database: Institute for Fermentation, Osaka

URL: http://www.ifo.or.jp/index_e.html

ID example 3189

IMGT_GENE-DB:

Database: Immunogenetics database, immunoglobulin and T-cell receptor genes

URL: http://imgt.cines.fr

NCBI db_xref IMGT/GENE-DB
ID example IGKC

IMGT_HLA:

Database: Immunogenetics database, human MHC

URL: http://www.ebi.ac.uk/imgt/hla/

NCBI db_xref IMGT/HLA
ID example HLA00031

IMGT_LIGM:

Database: Immunogenetics database, immunoglobulins and T-cell receptors

URL: http://imgt.cines.fr

NCBI db_xref IMGT/LIGM
ID example U03895

InChI:

Primary subject chemical compound
ID type self-describing identifier
ID format canonicalized formula with ordered layers separated by /
ID example 1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
ID subject caffeine
ID regexp [-+/.,*;()?A-Za-z0-9]+

Editorial Notes

INSD:

Database: International Nucleotide Sequence Database Collaboration (GenBank, EMBL, DDBJ)

URL: http://www.insdc.org/

Primary subject nucleotide sequence
ID type accession number
ID format uppercase letters, followed by digits and optional .version suffix; e.g. LNNNNN, LLNNNNNN
ID example J01749
ID subject Cloning vector pBR322, complete genome
ID regexp [A-Z]+[0-9]+([.][0-9]+)?
URL prefix http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=
URL prefix http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=
URL prefix http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=
RNEF property GenBank ID

IntAct:

Database: IntAct protein interaction database

URL: http://www.ebi.ac.uk/intact/

ID example EBI-17086
URL prefix http://www.ebi.ac.uk/intact/search/do/search?searchString=

InterPro:

Database: InterPro protein sequence database

URL: http://www.ebi.ac.uk/interpro/

NCBI db_xref Interpro
ID example IPR002928
URL prefix http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=

IPI:

Database: International Protein Index

URL: http://www.ebi.ac.uk/IPI/IPIhelp.html

ID example IPI00000005.1

ISBN:

Database: International Standard Book Number

URL: http://isbntools.com/

ID example 0781702534
URL prefix http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=

ISFinder:

Database: Insertion sequence elements database

ID example ISA1083-2

ISSN:

Database: International Standard Serial Number

URL: http://www.issn.org/

ID example 1234-1231

IUPHAR:

Database: The IUPHAR Compendium of Receptor Characterization and Classification

ID example 2.1.CBD

JCM:

Database: Japan Collection of Microorganisms

URL: http://www.jcm.riken.go.jp/

ID example 1339

KEGG:

Redirect via regexp: pattern ([a-z]+)[:](.*) template KEGG_\1:\2

KEGG_COMPOUND:

Database: Kyoto Encyclopedia of Genes and Genomes

URL: http://www.genome.ad.jp/kegg/

Primary subject chemical compound
ID type accession number
ID format C followed by 5 digits
ID example C00074
ID subject Phosphoenolpyruvate
ID regexp C[0-9]{5}
URL prefix http://www.genome.ad.jp/dbget-bin/www_bget?cpd:

KEGG_cpd:

Redirect to: KEGG_COMPOUND:

KEGG_dr:

Redirect to: KEGG_DRUG:

KEGG_DRUG:

Database: Kyoto Encyclopedia of Genes and Genomes

URL: http://www.genome.ad.jp/kegg/

Primary subject drug
ID type accession number
ID format D followed by 5 digits
ID example D00245
ID subject Bisacodyl (JP14/USP)
ID regexp D[0-9]{5}
URL prefix http://www.genome.ad.jp/dbget-bin/www_bget?dr:

KEGG_ec:

Redirect to: EC:

KEGG_hsa:

Redirect to: GeneID:

KEGG_mmu:

Redirect to: GeneID:

KEGG_path:

Redirect to: KEGG_PATHWAY:

KEGG_PATHWAY:

Database: Kyoto Encyclopedia of Genes and Genomes

URL: http://www.genome.ad.jp/kegg/

Primary subject pathway
ID type accession number
ID format lowercase letters, followed by 5 digits
ID example ot00020
ID subject Citrate cycle (TCA cycle)
ID regexp [a-z]+[0-9]{5}
URL prefix http://www.genome.ad.jp/dbget-bin/www_bget?path:
URL prefix http://www.genome.ad.jp/dbget-bin/www_bget?path:

KEGG_rno:

Redirect to: GeneID:

LIGAND:

Database: KEGG LIGAND Database

URL: http://www.genome.ad.jp/kegg/docs/upd_ligand.html#COMPOUND

ID example 1.1.1.1
URL prefix http://www.genome.ad.jp/dbget-bin/www_bget?ec:
URL prefix http://www.genome.ad.jp/dbget-bin/www_bget?cpd:

Editorial Notes

LocusID:

Redirect to: GeneID:

MaizeGDB:

Database: MaizeGDB

URL: http://www.maizegdb.org

ID example 881225
URL prefix http://www.maizegdb.org/cgi-bin/id_search.cgi?id=

MaizeGDB_Locus:

Database: MaizeGDB

URL: http://www.maizegdb.org

ID example ZmPK1
URL prefix http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=?

MEDLINE:

Database: The Medline literature database

ID example 20572430

Editorial Notes

MEROPS:

Database: MEROPS - the Peptidase Database

URL: http://merops.sanger.ac.uk/

ID example A01.001

MEROPS_fam:

Database: MEROPS: The Peptidase Database

URL: http://merops.sanger.ac.uk/

ID example M18
URL prefix http://merops.sanger/ac/uk/famcards/

Editorial Notes

MeSH:

Database: Medical Subject Headings

URL: http://www.nlm.nih.gov/mesh/2005/MBrowser.html

ID example mitosis
URL prefix http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=

Editorial Notes

MetaCyc:

Database: The Metabolic Encyclopedia of metabolic and other pathways

URL: http://metacyc.org/

ID example GLUTDEG-PWY
URL prefix http://biocyc.org:1555/META/new-image?object=

MGD:

Database: Mouse Genome Database

URL: http://www.informatics.jax.org/

ID example Adcy9
URL prefix http://www.informatics.jax.org/searches/marker.cgi?

MGI:

Database: Mouse Genome Informatics

URL: http://www.informatics.jax.org/

Primary subject gene
ID type sequential identifier
ID format positive numeral
ID example 98834
ID subject transformation related protein 53
ID regexp [1-9][0-9]*
URL prefix http://www.informatics.jax.org/searches/accession_report.cgi?id=
URL prefix http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:
RNEF property MGI ID

MIM:

Redirect to: OMIM:

Editorial Notes

MIPS_funcat:

Database: MIPS Functional Catalogue

URL: http://mips.gsf.de/proj/funcatDB/

ID example 11.02
URL prefix http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=

MO:

Database: The MGED Ontology

URL: http://mged.sourceforge.net/ontologies/MGEDontology.php

ID example Action
URL prefix http://mged.sourceforge.net/ontologies/MGEDontology.php#

NASC_code:

Database: Nottingham Arabidopsis Stock Centre Seeds Database

URL: http://arabidopsis.info

ID example N3371
URL prefix http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=

NCBI_GB:

Redirect to: INSD:

NCBI_GP:

Database: NCBI GenPept

URL: http://www.ncbi.nlm.nih.gov/

ID example EAL72968
URL prefix http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=

NCBI_NM:

Database: NCBI RefSeq

URL: http://www.ncbi.nlm.nih.gov/

ID example 123456

Editorial Notes

NCBI_NP:

Database: NCBI RefSeq

URL: http://www.ncbi.nlm.nih.gov/

ID example 123456

Editorial Notes

NextDB:

Database: Nematode Expression Pattern DataBase

URL: http://nematode.lab.nig.ac.jp/

ID example CELK01662

niaEST:

Database: NIA Mouse cDNA Project

URL: http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html

ID example L0304H12-3

OMIM:

Database: Online Mendelian Inheritance in Man database

URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

Primary subject gene
Subject gene-related genetic disorders
ID type sequential identifier
ID format positive numeral
ID example 191170
ID subject TUMOR PROTEIN p53
ID regexp [1-9][0-9]*
URL prefix http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?
URL prefix http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=
RNEF property OMIM ID

PDB:

Database: Protein Data Bank

URL: http://www.rcsb.org/pdb/

ID example 1A4U
URL prefix http://www.rcsb.org/pdb/cgi/explore.cgi?pid=223051005992697&pdbId=

Pfam:

Database: Pfam: Protein families database of alignments and HMMs

URL: http://www.sanger.ac.uk/Software/Pfam/

ID example PF00046
URL prefix http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?

PfamB:

Database: Pfam-B supplement to Pfam

URL: http://www.sanger.ac.uk/Software/Pfam/

ID example PB014624

PGN:

Database: Plant Genome Network

URL: http://pgn.cornell.edu

ID example aam01-1ms3-a05

PIR:

Database: Protein Information Resource

URL: http://pir.georgetown.edu/

Primary subject protein
ID type accession number
ID format uppercase letters, followed by digits
ID example S02192
ID subject cellular tumor antigen p53 - rat
ID regexp [A-Z]+[0-9]+
URL prefix http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=
RNEF property PIR ID

PIRSF:

Database: PIR Superfamily Classification System

URL: http://pir.georgetown.edu/pirsf/

ID example SF002327
URL prefix http://pir.georgetown.edu/cgi-bin/ipcSF?id=

PMID:

Database: PubMed

URL: http://pubmed.gov/

Primary subject article
ID type sequential identifier
ID format positive numeral
ID example 16446403
ID subject Mol Cancer Res. 2006 Jan;4(1):15-25.
ID regexp [1-9][0-9]*
URL prefix http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=

PO:

Database: Plant Ontology Consortium Database

URL: http://www.plantontology.org/

ID example 0009004
URL prefix http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=

Editorial Notes

Pompep:

Database: Schizosaccharomyces pombe protein data

ID example SPAC890.04C

PRINTS:

Database: PRINTS compendium of protein fingerprints

URL: http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/

ID example PR00025
URL prefix http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?cmd_a=Display&qua_a=none&fun_a=Text&qst_a=

ProDom:

Database: ProDom protein domain families automatically generated from Swiss-Prot and TrEMBL

URL: http://prodes.toulouse.inra.fr/prodom/current/html/home.php

ID example PD000001
URL prefix http://prodes.toulouse.inra.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=

Prosite:

Database: Prosite. Database of protein families and domains

URL: http://www.expasy.ch/prosite/

ID example PS00365
URL prefix http://www.expasy.ch/cgi-bin/prosite-search-ac?

protein_id:

Redirect to: INSD:

PSEUDO:

Database: EMBL pseudo protein identifier

ID example CAC44644.1

PubChem_Compound:

Database: NCBI PubChem database of chemical structures

URL: http://pubchem.ncbi.nlm.nih.gov/

Primary subject chemical compound
ID type sequential identifier
ID format positive numeral
ID example 2519
ID subject Caffeine
ID regexp [1-9][0-9]*
URL prefix http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=
URL prefix http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=

PubChem_Substance:

Database: NCBI PubChem database of chemical substances

URL: http://pubchem.ncbi.nlm.nih.gov/

Primary subject chemical substance
ID type sequential identifier
ID format positive numeral
ID example 199601
ID subject Coffee
ID regexp [1-9][0-9]*
URL prefix http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=
URL prefix http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=

RATMAP:

Database: Rat Genome Database

URL: http://ratmap.gen.gu.se/

ID example 5

Editorial Notes

Reactome:

Database: Reactome human pathway database

URL: http://www.reactome.org/

ID example 70635
URL prefix http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=

REBASE:

Database: REBASE, The Restriction Enzyme Database

URL: http://rebase.neb.com/rebase/rebase.html

ID example EcoRI
URL prefix http://rebase.neb.com/rebase/enz/

Editorial Notes

RESID:

Database: RESID Database of Protein Modifications

ID example AA0062

RGD:

Database: Rat Genome Database

URL: http://rgd.mcw.edu/

Primary subject gene
ID type sequential identifier
ID format positive numeral
ID example 3889
ID subject tumor protein p53
ID regexp [1-9][0-9]*
URL prefix http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=
RNEF property RGD ID

RGDID:

Redirect to: RGD:

RiceGenes:

Database: Rice database accession numbers

URL: http://www.gramene.org/

ID example AA231856

RNAmods:

Database: The RNA Modification Database

URL: http://medlib.med.utah.edu/RNAmods/

ID example 037
URL prefix http://medlib.med.utah.edu/cgi-bin/rnashow.cgi?

RZPD:

Database: Resource Centre Primary Database Clone Identifiers

URL: http://www.rzpd.de/

ID example IMAGp998I142450Q6

SGD:

Database: Saccharomyces Genome Database

URL: http://www.yeastgenome.org/

ID example S000006169
URL prefix http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=

SGD_LOCUS:

Database: Saccharomyces Genome Database

URL: http://www.yeastgenome.org/

ID example GAL4
URL prefix http://db.yeastgenome.org/cgi-bin/locus.pl?locus=

Editorial Notes

SGD_REF:

Database: Saccharomyces Genome Database

URL: http://www.yeastgenome.org/

ID example S000049602
URL prefix http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=

SMART:

Database: Simple Modular Architecture Research Tool

URL: http://smart.embl-heidelberg.de/

ID example SM00005
URL prefix http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=

SoyBase:

Database: Glycine max Genome Database

URL: http://soybase.agron.iastate.edu/

ID example Satt005

STKECM:

Redirect via regexp: pattern stkecm_([A-Z]+)_([0-9]+) template STKECM_\1:\2

STKECM_CMC:

Database: Science's STKE Connections Map

URL: http://stke.sciencemag.org/

Primary subject chemical substance
ID type sequential identifier
ID format positive numeral
ID example 15493
ID subject Acetylcholinesterase (AChE)
ID regexp [1-9][0-9]*
URL prefix http://stke.sciencemag.org/cgi/cm/stkecm;CMC_

STKECM_CMP:

Database: Science's STKE Connections Map

URL: http://stke.sciencemag.org/

Primary subject pathway
ID type sequential identifier
ID format positive numeral
ID example 10827
ID subject JNK MAPK Pathway
ID regexp [1-9][0-9]*
URL prefix http://stke.sciencemag.org/cgi/cm/stkecm;CMP_

SubtiList:

Database: Bacillus subtilis genome sequencing project

URL: http://genolist.pasteur.fr/SubtiList/

ID example BG10001

SUBTILISTG:

Database: Bacillus subtilis Genome Sequence Project

URL: http://genolist.pasteur.fr/SubtiList/

ID example accC

TAIR:

Database: The Arabidopsis Information Resource

URL: http://www.arabidopsis.org/

ID example gene:2062713
URL prefix http://www.arabidopsis.org/servlets/TairObject?accession=

Editorial Notes

taxon:

Database: NCBI's taxonomic identifier

URL: http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html

ID example 4932

Editorial Notes

TC:

Database: The Transport Protein Database

URL: http://tcdb.ucsd.edu/tcdb/

ID example 9.A.4.1.1
URL prefix http://tcdb.ucsd.edu/tcdb/tcprotein.php?substrate=

TGD_LOCUS:

Database: Tetrahymena Genome Database

URL: http://www.ciliate.org/

ID example PDD1
URL prefix http://db.ciliate.org/cgi-bin/locus.pl?locus=

Editorial Notes

TGD_REF:

Database: Tetrahymena Genome Database

URL: http://www.ciliate.org/

ID example T000005818
URL prefix http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=

TIGR_Ath1:

Database: The Institute for Genomic Research, Arabidopsis thaliana database

URL: http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml

ID example At3g01440
URL prefix http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=

TIGR_CMR:

Database: The Institute for Genomic Research, Comprehensive Microbial Resource

URL: http://www.tigr.org/

ID example VCA0557
URL prefix http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=

TIGR_EGAD:

Database: The Institute for Genomic Research, EGAD database

URL: http://www.tigr.org/

ID example 74462
URL prefix http://www.tigr.org/tigr-scripts/CMR2/ht_report.spl?prot_id=

TIGR_GenProp:

Database: The Institute for Genomic Research, Genome Properties

URL: http://www.tigr.org/

ID example GenProp0120
URL prefix http://www.tigr.org/tigr-scripts/CMR2/genome_property_def.spl?prop_acc=

TIGR_Pfa1:

Database: The Institute for Genomic Research, Plasmodium falciparum database

URL: http://www.tigr.org/tdb/e2k1/pfa1/pfa1.shtml

ID example PFB0010w
URL prefix http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=pfa1&orf=

TIGR_REF:

ID example GO_ref

Editorial Notes

TIGR_Tba1:

Database: The Institute for Genomic Research, Trypanosoma brucei database

URL: http://www.tigr.org/tdb/e2k1/tba1/

ID example 25N14.10
URL prefix http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=tba1&orf=

TIGR_TGI:

Database: The Institute for Genomic Research, TIGR Gene Index

URL: http://www.tigr.org/

ID example Cattle_TC123931
URL prefix http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=?

TIGR_TIGRFAMS:

Database: The Institute for Genomic Research, TIGRFAMs HMM collection

URL: http://www.tigr.org/

ID example TIGR00254
URL prefix http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?acc=

TrEMBL:

Database: UniProtKB-TrEMBL, a computer-annotated protein sequence database supplementing UniProtKB and containing the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database but not yet integrated in UniProtKB/Swiss-Prot

URL: http://www.uniprot.org

ID example O31124
URL prefix http://www.ebi.uniprot.org/entry/

UM-BBD_enzymeID:

Database: The University of Minnesota Biocatalysis/Biodegradation Database

URL: http://umbbd.ahc.umn.edu/index.html

ID example e0413
URL prefix http://umbbd.ahc.umn.edu:8007/umbbd/servlet/pageservlet?ptype=ep&enzymeID=

UM-BBD_pathwayID:

Database: The University of Minnesota Biocatalysis/Biodegradation Database

URL: http://umbbd.ahc.umn.edu/index.html

ID example acr
URL prefix http://umbbd.ahc.umn.edu/

Editorial Notes

UniGene:

Database: NCBI's UniGene database

URL: http://www.ncbi.nih.gov/UniGene

Primary subject cluster of nucleotide sequences
ID type sequential identifier (organism-specific)
ID format 2/3-letter organism abbreviation followed by dot and positive numeral
ID example Hs.408312
ID subject p53 cluster
ID regexp ([A-Z][a-z][a-z]?)[.]([1-9][0-9]*)
URL regexp http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=\1\&CID=\2
URL prefix http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=
RNEF property Unigene ID

UNILIB:

Database: Unified Library Database, a library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap

ID example 1002

UniParc:

Database: UniProt Archive; a non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office

URL: http://www.ebi.ac.uk/uniparc/

ID example UPI000000000A
URL prefix http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=

UniProt:

Database: The Universal Protein Knowledgebase, a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR

URL: http://www.uniprot.org/

NCBI db_xref UniProtKB/Swiss-Prot
Primary subject protein
ID type accession number
ID format 6 alphanumerical characters
ID example P08251
ID subject Sodium/potassium-transporting ATPase beta-1 chain
ID regexp [OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]
URL prefix http://www.ebi.uniprot.org/entry/
RNEF property Swiss-Prot Accession

UniProtKB_Swiss-Prot:

Database: section of the UniProt Knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature

URL: http://www.uniprot.org

NCBI db_xref UniProtKB/Swiss-Prot
ID example P12345

Editorial Notes

UniProtKB_TrEMBL:

Database: section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation

URL: http://www.uniprot.org

NCBI db_xref UniProtKB/TrEMBL
ID example Q00177

VBASE2:

Database: Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse

URL: http://www.dnaplot.de/vbase2/vbase2.php

ID example humIGKV165

WB:

Database: WormBase, database of nematode biology

URL: http://www.wormbase.org/

ID example lin-12
URL prefix http://www.wormbase.org/db/get?class=Locus;name=

WB_REF:

Database: WormBase, database of nematode biology

URL: http://www.wormbase.org/

ID example cgc467
URL prefix http://www.wormbase.org/db/misc/paper?name=

Editorial Notes

WorfDB:

Database: C. elegans ORFeome cloning project

URL: http://worfdb.dfci.harvard.edu/

ID example pos-1

WormBase:

Database: Caenorhabditis elegans Genome Database

URL: http://www.wormbase.org/

ID example R13H7

WP:

Database: Wormpep, database of proteins of C. elegans

URL: http://www.wormbase.org/

ID example CE25104
URL prefix http://www.wormbase.org/db/get?class=Protein;name=

Editorial Notes

ZFIN:

Database: The Zebrafish Information Network

URL: http://zfin.org/

ID example ZDB-GENE-990415-103
URL prefix http://zfin.org/cgi-bin/ZFIN_jump?record=